If you fail to file your VAT return by the deadline, the Egyptian Tax Authority (ETA) has the right to assess the tax themselves for that period, based on whatever information or basis they determine to be appropriate (Article 14). This means the ETA will estimate how much VAT you owe, and you will be liable for that amount — plus any applicable penalties outlined elsewhere in the law.
The ETA generally has up to three years from the end of the filing period to review and amend your tax return. If they attempt to amend your return and charge additional tax after this three-year window has passed, they are restricted from charging additional tax for the period beyond those elapsed three years (Article 15). This provides some protection against very old reassessments, but it is not a reason to delay filing — penalties and interest can accumulate quickly.
As an expat running a business in Egypt, the best practice is to work with a qualified Egyptian accountant to ensure your VAT returns are filed accurately and on time each period. Keeping thorough records of all taxable sales and purchases will also protect you in the event of an ETA audit or reassessment. Smuggled goods or sales made contrary to applicable laws are also subject to VAT at the rates effective on the date of the offense (Article 9), so compliance across all aspects of your business is essential.
This is general legal information, not legal advice. For advice on your specific situation, consult a lawyer licensed in Egypt.