A medical bulletin from Roland Garros organisers said Becker had suffered a pectoral muscle injury during a five-set defeat of 32nd seed Fernando Verdasco of Spain on Wednesday.
US Open runner-up Nishikori beat Brazil’s Thomaz Bellucci and is yet to drop a set as he looks to better his previous run at Roland Garros, when he also reached the last 16 in 2013 before losing to Rafael Nadal.
He will face either Lukas Rosol of the Czech Republic or Teymuraz Gabashvili of Russia for a place in the quarter-finals.
“Very sorry to hear about Benjamin being injured. I hope he recovers fast,” tweeted Nishikori, who also made the fourth round in 2013.
Becker, 33, needed two gruelling five-setters to get to the third round, seeing off Ruben Bemelmans of Belgium and Spanish 32nd seed Fernando Verdasco.