Foreign Affairs Minister John Baird told the Toronto Star in an email the decision was made because for three days, rioters have targeted the U.S. Embassy, just 400 yards away.
"As a security precaution, and to ensure the protection of Canadian staff, we have closed our Embassy in Cairo for the day," Baird wrote.
Because the Muslim weekend is Friday and Saturday, it's unlikely the embassy would reopen until at least Sunday, CTV News said.
Turmoil broke out in Muslim countries Tuesday, the anniversary of the Sept. 11 terrorist attacks on New York and Washington, when a film trailer ridiculing the Prophet Muhammad that was posted on YouTube gained widespread attention.
Protesters stormed the U.S. Embassy in Benghazi, Libya, killing Ambassador Chris Stevens and three others. Egyptian protesters have also targeted the American facility in Cairo and demonstrators stormed the U.S. Embassy in Sanaa, Yemen, Thursday.
Egyptian President Mohammed Morsi said his security forces would not allow a repeat of the killings in Libya.
"The Egyptian state is responsible for protecting embassies and consulates, and the Egyptian people will not engage in these ... unlawful acts," he said.