The world number 17 has already ruled himself out of the forthcoming Masters 1000 tournaments in Madrid and Rome.
With the latter finishing just a week before the action begins at Roland Garros, Nishikori must be considered doubtful to play in the second Grand Slam event of the season.
The Japanese wrote on his Facebook page: "(I) injured my stomach during my last match in Barcelona.
"(I am) seeing doctors this week and will see how long the healing takes. Madrid and Rome are going to be out for sure. Will keep everyone posted in the next weeks on how things go."
The 22-year-old, who reached the quarter-finals of the Australian Open earlier this season, will be particularly disappointed having shown some decent form on the claycourts in recent weeks.
He made the last eight in Barcelona before being forced to retire with the injury against Fernando Verdasco. The previous week Nishikori reached the last 16 in Monte Carlo.
The French Open starts on May 27.