Pupils at the lycées Henry IV, Condorcet and Louis le Grand were evacuated while searches of the premises took place.
Six schools in central France's Lyon were also evacuated, after someone called and said "You will all die", reported the Liberation newspaper.
Police were called out after the threats were made, but all turned out to be hoaxes.
The tweet below for Paris education chiefs said pupils had been taken to a safe place while police secured the school.
The same Paris schools were the subject of hoax bomb threats on two separate occasions last week, when eight lycées across the French capital were evacuated.
Each time pupils were confined to a safe place while searches were carried out. In each case nothing was found and the calls were treated as hoaxes.
With France still on high alert after the November attacks the threats, which have been made via anonymous phone calls have been treated seriously by police and education authorities.
Fears were also raised when the Isis group's French-language magazine Dar-al-Islam called in its November edition for its followers to kill teachers in the French education system, describing them as "enemies of Allah".