The controls will "respect the principle of proportionality", the ministry said in a note to the European Union.
The 1985 Schengen agreement ended passport checks and other measures on borders but France resumed them with neighbours such as Italy and Belgium after the November 2015 Paris attacks.
Anti-terror bill passed by lower house
The National Assembly on Wednesday agreed to make several measures from the state of emergency declared at the time permanently part of French law.
The government's anti-terror law was passed on a second reading by the lower house but must still be approved by the Senate.
It will make permanent powers that are currently temporary, facilitating the authorities' right to search premises, assign people to limited movement areas, closing places of worship judged nests of terror and making identity checks at borders.
MPs voted down a motion to reject the law, moved by the mainstream right on the grounds that the state of emergency should not be ended and supported by some on the left for "diametrically opposed reasons" of concern over civil liberties.