He held a two-hour meeting with club president, Josep Bartomeu, on Wednesday, where he was told his job is safe.
Abidal had granted an interview, in which he claimed that some members of the squad, did not work hard enough under former manager Ernesto Valverde.
Messi fired back in an Instagram post, in which he told the Frenchman to name names and face his work.
The clash led to tensions at the club, with speculation that Messi could leave the Camp Nou.
However, it is understood Bartomeu spoke to Messi before his meeting with Abidal and that tensions at the club have now eased.