Annual Return, Beneficial Owner, Financial Statements: What Your Company Secretary Files vs What You Still Owe LHDN

Your company secretary files your Annual Return, your Beneficial Owner declaration, and your Financial Statements with SSM (Suruhanjaya Syarikat Malaysia, the Companies Commission of Malaysia). Your company secretary does NOT file your taxes. Estimated tax (CP204), Form C (yearly corporate tax return), and Form E/EA for your staff all go to LHDN (Lembaga Hasil Dalam Negeri, the Inland Revenue Board), and that part stays on you or your tax agent. Mixing these two filing tracks up is one of the most common and most costly mistakes a first-time Sdn Bhd owner makes, because SSM and LHDN run on separate deadlines, separate penalty systems, and separate portals.

🔔 TL;DR

SSM filings (Annual Return, Financial Statements, Beneficial Owner declaration) are handled with your company secretary’s help; LHDN filings (CP204, Form C, Form E/EA) are a separate obligation you or your tax agent must manage.
Annual Return is due generally within 30 days of your incorporation anniversary (Section 68); a default can attract a fine of up to RM50,000.
Financial Statements and LHDN’s Form C run on different deadlines and different portals, so lodging one does not fulfil the other.
Beneficial Owner information must be lodged through e-BOS within 14 days after it is recorded in the company’s register, and non-compliance can attract penalties under the Companies Act.
Small companies that qualify for audit exemption may be able to file Unaudited Financial Statements through MBRS (Malaysian Business Reporting System) instead of a full audit, but this does not remove any LHDN tax obligation.

📌 What does a company secretary file with SSM?

A qualified company secretary supports the recurring SSM filings a Sdn Bhd needs to stay compliant, including the Annual Return, the Beneficial Owner declaration or updates, and the Financial Statements. None of these are optional, and none of them pause just because your business is small or quiet for the year.

Annual Return (Section 68 of the Companies Act 2016): a snapshot of your company as at the anniversary of incorporation. It includes your company name, registration number, registered address, principal business activities, director and shareholder details, and shareholding structure.
Beneficial Owner (BO) declaration: a declaration naming the natural person or persons who ultimately own or control the company through shares and effective interest. A person can count as a beneficial owner even with less than 20% of shares if they exercise significant influence or control.
Financial Statements: your company’s financial position and performance for the year, lodged via MBRS in XBRL format (a structured data format SSM requires for digital filing), either audited or unaudited depending on whether you qualify for audit exemption.

These filings keep your company “alive” on the public register. A company secretary in Kuala Lumpur or anywhere else in Malaysia prepares and submits them on your behalf, but the underlying obligation to have accurate records sits with the company and its directors.

📌 What is the beneficial owner declaration and why does SSM care?

Building on the filings above, the Beneficial Owner declaration deserves its own explanation because it’s the newest and most misunderstood of the three. Under Malaysian law, a beneficial owner is a natural person who ultimately owns or controls a company, whether directly through shares or indirectly through effective control. Since April 1, 2024, every company incorporated or registered in Malaysia must report its beneficial owners to SSM. A newly incorporated private company generally must obtain and record its beneficial ownership information within 60 days from the first company secretary’s appointment, and then lodge that information with the Registrar through e-BOS within 14 days of the record being made.

Here is the part that trips people up: this is not a one-time form. Any change to who owns or controls the company, for example a new investor coming in, a shareholder exiting, or a change in who holds decision-making power, must be recorded in the company’s register, and the updated information must then be lodged with the Registrar through e-BOS (the Beneficial Ownership System) within 14 days of that record being made. For companies with anniversary dates from December 1, 2024 onward, this update must happen before the Annual Return is lodged. Non-compliance can attract penalties under the Companies Act, so this is not a box you tick once and forget.

📌 How is the Annual Return different from the Financial Statements?

A related but distinct question is why SSM asks for two separate documents when both seem to describe “the state of the company.” The Annual Return is about structure: who runs the company, who owns it, where it’s registered. The Financial Statements are about numbers: revenue, expenses, assets, liabilities, profit or loss.

Filing	What it covers	Generally due	Maximum penalty upon conviction
Annual Return (Section 68)	Company structure, directors, shareholders, MSIC business codes	Within 30 days of incorporation anniversary	Fine of up to RM50,000 against the company and officers in contravention
Financial Statements (Section 259)	Financial position and performance, audited or unaudited	As prescribed under the Companies Act 2016, unless an extension is approved	Fine of up to RM250,000 upon conviction
Beneficial Owner update	Who owns or controls the company	Within 14 days of the change being recorded in the company’s register; lodged via e-BOS before the Annual Return	Fine of up to RM300,000 upon conviction

Separately from these court fines, SSM also charges late-lodgement penalties that range from RM50 to RM200 per document depending on how late it is. These are administrative penalties, not court fines, so don’t add the two together when estimating your risk.

📌 Does audit exemption remove any of these SSM obligations?

Stepping back from the deadline mechanics, a common point of confusion is what audit exemption actually changes. Audit exemption (Section 267(2) of the Companies Act 2016, together with SSM’s qualifying criteria) only decides whether your Financial Statements need to be audited by an external auditor before lodging. It does not remove the requirement to have a company secretary, to keep proper accounting records, or to prepare and lodge Financial Statements at all.

In practical terms: if your company’s revenue stays under the applicable threshold, sustained over the current and prior two financial years, you may be able to file Unaudited Financial Statements (UAFS) through MBRS instead of a full audited set. You still need to appoint an auditor if you don’t qualify, and you still file on the same SSM timeline either way. This has no bearing on your separate LHDN tax obligations.

📌 What does your company secretary NOT file, and why does LHDN run separately?

This is the core distinction the title promises, and it’s worth being precise about it. LHDN tax filing requirements run on an entirely different clock from SSM’s:

CP204 (Estimated Tax): due within 3 months of your financial year beginning.
Form C (Final Corporate Tax Return): due according to LHDN’s prescribed deadline after your financial year end.
Form E and EA: annual employer and employee tax reporting for your staff, separate again from both of the above.

Compare this to SSM’s Annual Return (30 days from incorporation anniversary) and Financial Statements deadlines. These are different deadlines, governed by two different regulators, with two different portals. LHDN applies its own penalty regime for late tax filing, and these penalties are entirely separate from SSM’s fines and late-lodgement penalties. A company secretary’s scope of work covers the SSM side. Tax filing with LHDN needs your own tax agent or accountant, even though many companies choose to use one provider for both so the two tracks don’t fall out of sync.

📌 Frequently Asked Questions

Does a vacant company secretary position pause my Annual Return deadline?

No. A vacant position does not pause or suspend Annual Return, Beneficial Owner, or Financial Statement deadlines. Your obligations continue, and directors should make sure the information is collected and submitted on time.

Can I use my own external auditor even with a digital company secretary?

Yes. Audit exemption or not, you’re free to keep your own external auditor or tax agent while using a digital company secretary platform for your SSM filings.

Is beneficial owner declaration a one-time filing?

No. The initial declaration is followed by mandatory updates whenever ownership or control changes, lodged through e-BOS within 14 days after the change is recorded in the company’s register.

What’s the difference between Section 68 and Section 259 of the Companies Act 2016?

Section 68 governs the Annual Return (company structure and details). Section 259 governs Financial Statements (financial position and performance).

If my company qualifies for audit exemption, do I still need a company secretary?

Yes. Audit exemption only affects whether your Financial Statements need an auditor’s sign-off. It does not remove the statutory requirement to appoint a qualified company secretary under Section 235.

Does SSM filing fulfil my LHDN tax obligations?

No. Filing your Annual Return and Financial Statements with SSM has no bearing on your CP204 or Form C obligations with LHDN. These are separate filings with separate deadlines and separate penalty regimes.

ABOUT BOSS BOLEH

Boss Boleh is an online company secretary and compliance platform built for first-time Sdn Bhd owners. Beyond company secretarial work, it also offers a one-stop compliance solution for entrepreneurs, including accounting, tax planning and tax filing services. We handle Annual Return and Beneficial Owner submissions to SSM, and you’re free to keep your own external auditor or tax agent. With over 1,500 Google reviews at a 4.9-star average, we support clients in Kuala Lumpur, every other state in Malaysia, and Malaysians living overseas.