Martial was left out of the United squad for Saturday’s draw with Stoke and reportedly travelled back to France after being given permission to take some time off.
The incident fuelled speculation over Martial’s future but the Red Devils boss insists he has no problem with the 22-year-old’s trip.
United take on Wigan in the FA Cup on Sunday and Mourinho has revealed more players could be heading away, including No.1 David De Gea.
“I give the players this freedom of choice, so no problem at all with Anthony to go to Paris. That’s completely fine,” he said.