The anti-Syrian movement is tied to the Christian right
"The banned groups are forbidden in any form from holding meetings and demonstrations or distributing leaflets, pamphlets or bulletins," said a statement from the Central Security Council - which controls Lebanon's various security forces.
The announcement follows the rounding-up by the armed forces of about 200 Christians belonging to the groups which held a rally last weekend calling on Syria to leave Lebanon.
The government later said it backed the detentions, although it admitted it had no knowledge of them beforehand.
Information Minister Ghazi Aridi said the cabinet had praised the army for maintaining civil order.
The detentions have sparked fears that Lebanon is turning into a police state where security forces are not accountable to the government.
The official National News Agency said that 23 of the detainees had been handed to the military investigative judge, 18 were sent to the military court and 20 turned over to the general attorney.
Opposition opposed
Those arrested on Tuesday were mainly followers of the Free National Current, FNC, which is tied to the exiled Christian leader Michel Aoun and the Lebanese Forces, a disbanded Christian militia.
Its leader, Samir Geagea, is in jail.
From his home in France, General Aoun urged his supporters to continue protesting the Syrian military presence.
Syria has had some 35,000 troops in Lebanon since 1975.
Most of those arrested were students, but there were also a number of political leaders among them.
They included Toufic Hindi, a leading member of the Lebanese Forces who was picked up from his home without a warrant, as well as the head of the FNC, former general Nadim Lteif.
Correspondents say around 50 of those detained have since been released, but that leaders are still being held.