The Egyptian military said one of its navy vessels came under "terrorist" attack in the Mediterranean on Wednesday, leaving eight servicemen missing at sea.
The military said in a statement that four boats used by the assailants were destroyed and 32 of the suspected militants were arrested.
The Egyptian government is fighting an Islamist militant insurgency that has killed scores of policemen and soldiers, but a maritime attack is unprecedented.
An earlier report on the official MENA news agency reported that a naval vessel has been set alight in an exchange of fire with assailants about 70 kilometres (45 miles) from Egypt's shore.
The military said it was a "terrorist" attack.
"Search and rescue operations have evacuated five wounded servicemen to a military hospital... and there are still eight personnel lost and the search continues," it said in the statement.
The military said it destroyed "four boats used by the armed assailants, including terrorists, and arrested 32 people".