The Argentina international played a starring role as Barca twice came from behind to beat Villarreal 3-2 in La Liga on Sunday, scoring the third and ultimately decisive goal.
Messi - who has 22 league goals this term - did not partake in the club's recovery session, although Barca did not elaborate on the reasons why.
"The first team has trained on Monday morning at the Ciutat Esportiva Joan Gamper," read a statement on Barcelona's website.
"A few hours after the 3-2 win over Villarreal in La Liga, the players have carried out work of recovery.
"Neymar, Dani Alves and Douglas have carried out specific work, while Leo Messi has not been training due to personal issues, with the permission of the club."
Reports earlier this season suggested that Messi was contemplating a surprise exit from Camp Nou due to a troubled relationship with head coach Luis Enrique.
Barca centre-back Jeremy Mathieu revealed last week that Messi and Luis Enrique were involved in a training ground bust-up when the players returned from their mid-season break at the start of last month.
The Frenchman claimed that Messi was left incensed after being on the receiving end of a hefty challenge during a training match, but Mathieu claimed the issue was swiftly resolved.
