French military officials said the three were members of a force of 95 gendarmes guarding French diplomatic installations and personnel.
Under international law, Peru has jurisdiction over foreign diplomatic installations but is not supposed to exercise its powers without permission from the foreign government that occupies a particular property.
American officials objected because they said it suggested that NATO had intentionally attacked the embassy, a diplomatic installation that under international law cannot be targeted.
And, the official said, attacking American military or diplomatic installations - by now well versed in facing Middle Eastern terrorism - "is not going to be an easy task."
Officials said that when the Aug. 11 instructions were issued, they could not recall a similar instance when several American diplomatic installations suspended operations simultaneously.
The panels criticized the United States Government as relying too heavily on intelligence about specific terrorist threats in determining which embassies and other diplomatic installations deserved protection.
Embassy Row is the informal name for a street or area of a city in which embassies or other diplomatic installations are concentrated.
The State Department ordered a tightening of security at American embassies and other diplomatic installations around the world.
Officials said they could not recall a similar instance in recent years in which several American diplomatic installations, which often get threats of violence, had suspended operations simultaneously.
The United States has announced a worldwide alert for embassies and other diplomatic installations after the terrorist attacks last week.