The Chadian military said on Saturday that it had captured more than 250 rebels during an operation against fighting militias from Libya.
A statement states that the large number included "four leaders" who had been arrested.
They said that 40 of the rebels' vehicles had been destroyed and hundreds of weapons confiscated.
France, which is providing military support to Chad, deployed fighter jets this week to attack the convoy in the Ennedi region.
On Thursday, she announced that she had attacked the vehicle power several times this week in connection with the Chadian armed forces.
The militants had managed to get hundreds of kilometers into the country before they were stopped, reports AFP.
Intelligence officials who spoke with the Reuters news agency said only 100 fighters had been arrested.
The slump is the latest in a series of threats against the rule of President Idriss Déby.
French troops are currently deployed in Chad as part of Operation Barkhane – a continuing coalition effort in the African Sahel to fight the jihadists.
France dominated Chad as a colony from 1900 until it became independent in 1960 and previously supported President Déby.
A rebel coalition known as the Union of Resistance forces (UFR) says it was behind the recent convoy.
The Alliance is made up of smaller rebel groups opposing the presidency of Déby.
Local media say UFR Chief of Staff Ousman Teguene may be among those detained.
The Chadian military announced the arrest and said that it would continue its operation against rebels in the Ennedi region.
President Déby has been in office since 1990 when he took control in a coup.
Last year, the Chadian parliament approved a new constitution that would expand its powers and enable it to remain in office until 2033.