The move comes amid increasing attacks by Islamist militants in Egypt and calls from the extremist Islamic State group for attacks on Western targets.
The Canadian embassy said in a statement that it would be closed "due to security reasons" today, with a separate email to Canadian citizens in Egypt saying this would be the case "until further notice".
The British embassy also remained closed after shutting its public services yesterday.
British Ambassador John Casson said the decision had been taken "to ensure the security of the embassy and our staff".
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Both countries have previously issued warnings to their citizens against travel to restive areas of Egypt including parts of the Sinai Peninsula, where the Ansar Beit al-Maqdis militant group has pledged allegiance to IS.
Meanehile the embassy of the United States in Cairo remained open today.
Foreign missions have stepped up security measures since last year's ouster of Islamist president Mohamed Morsi prompted a rise in militant attacks targeting Egyptian security forces.
No foreign missions nor interests have so far been directly targeted.
Most attacks have been in the Sinai Peninsula, but several
Islamic State (IS), which has captured swathes of territory in Iraq and Syria, has called on affiliate groups to target foreign nationals and interests in their countries, especially citizens of countries belonging to a US-led coalition fighting IS.
Both Britain and Canada have joined the coalition.