The 25-year-old, who was runner-up at last year’s US Open, was due to play Colombia’s Santiago Giraldo in the second match on Centre Court on Wednesday.
That second-round match was replaced on the main show court programme by Croatian ninth seed and US Open champion Maric Cilic’s match against Lithuanian Ricardas Berankis.
Nishikori carried the injury into Wimbledon but won his opening match against Italy’s Simone Bolelli in five sets.
“It got better before the first match and I thought it was going to be okay but in the last match, in the fifth set, I was hurting too much,” Nishikori said.
He tried to practise on Wednesday but felt too much pain.
“I decided not to play today,” Nishikori said. “It’s not a big injury, just a little tear.
“It’s very disappointing. I thought I was playing well on grass. I’m unfortunate to lose this chance.”