The Brazil international, who missed the Copa America due to injury, was absent for last week's Ligue 1 opener against Nimes, during which some supporters protested against the forward.
Neymar reported late for pre-season training and Leonardo has previously confirmed the 27-year-old wants to leave Paris, two years after he joined from Barcelona for a world-record €222million.
A return to Camp Nou has been mooted for Neymar, although Barca coach Ernesto Valverde was unwilling to discuss the prospect at a news conference on Thursday.
And Leonardo has denied reports Neymar remains injured and has been left out of Thomas Tuchel's group as a result.
"Things are simple," Leonardo said to RMC Sport.
"Neymar was monitored by several great doctors and surgeons early in the season and his fracture line is fully consolidated at the fifth metatarsal. Neymar's injury is completely healed.
"It's false. He is not removed from the group. He follows his personalised rehabilitation programme."
Neymar's future remains unresolved, though, with Barca and Real Madrid having reportedly failed with offers, and Leonardo has suggested the attacker may miss Sunday's trip to Rennes.
"He is a player of Paris Saint-Germain, there is still three years of his contract in Paris, we must not forget," Leonardo added.
"We must analyse everything, we must fix everything before he can play again.
"Neymar made mistakes. You know, I didn't know him. As the days go by, I get to know him.
"And I honestly think he's a good boy with a very good background. And on the pitch, he's an amazing player.
"There are discussions for his future, as you know it today, but nothing advanced."