PSG were held to a 1-1 draw at home to Lens which was enough to seal a 10th league title, but the club's ultras left the game with 15 minutes remaining instead of celebrating with the players.
When Neymar was asked about the fans leaving before the end of the game, he told ESPN Argentina: "It was surreal that part of the crowd left the stands. They're going to get tired of whistling, because I have another three years left on my contract."
Earlier this season, the Brazil international was subjected to jeers from his own supporters alongside teammate Lionel Messi after PSG's dramatic collapse against Real Madrid in the Champions League round-of-16 tie.
PSG captain Marquinhos also questioned the decision of the club's supporters and told Canal Plus: "The atmosphere is a shame. Football is our passion.
"We'll try to have as much fun as possible. It's a shame that won't be with the supporters, but we have to deal with it."
Marco Verratti added: "That's something I don't understand. I know that they were disappointed about Madrid, but at some point you have to move on."
PSG manager Mauricio Pochettino was less critical of the fan base after he secured the first league title of his managerial career.
"We are going through a difficult period with the fans and we hope it will get better," he said. "We're in a democracy and we accept all protests. But we have to show respect for this title."
Kylian Mbappe, who won the fifth Ligue 1 title of his short career, insisted that the supporters who left the stadium were in the minority.
"I'm not disappointed, if [the ultras] want to celebrate, they can do so; they don't want to, so they're not doing so," he told Canal Plus.
"The crowd was here, it's a minority who left. They're not representative of all of the supporters, but rather a minority. The stadium was full. We celebrated among ourselves in the dressing room; all that was missing was the cup. I'm savouring it."