The Brazilian damaged the fourth metatarsal in his left foot during Wednesday's Copa del Rey final defeat to Real Madrid, with the club confirming he could be out for up to four weeks.
With Barca's last game of the season - a potential La Liga title-decider at Atletico Madrid - in four weeks' time, the Argentinian is not convinced that Neymar will be able to return, while Carles Puyol will not face Athletic Bilbao on Sunday as he continues to struggle with a knee injury.
"It will be difficult to see him (Neymar) get a game," said the Barca coach.
"It will take about four weeks so I'm not optimistic that he'll play again this season for us."
The Catalan giants have lost all of their three previous matches - in three separate competitions - to dash Barca's hopes of a treble, with the spotlight heavily on Martino and his future at the club.
But Martino is reluctant to talk about what will happen at the end of the season, preferring to concentrate on the job in hand.
"I think all my focus has to be on this season," he said. "It's almost betraying the group thinking of being in charge next season when we're still not finished this season.
"We have to use all the strength that we've got to finish this season, then next season we'll see."
After Atletico's 2-0 win over Elche on Friday, Barca go into Sunday's game seven points behind the leaders and Martino concedes his side are relying heavily on results elsewhere.
"We have to understand that we still have a chance of winning the league and we have to hope teams above us slip up," he said.
"We can't depend on what we do so now it's a different situation. If the other teams do slip up it will be a great incentive for us."
