The Spain international announced the news on his official Instagram profile on Monday and will now miss the start of the new season.
"I want to let you know that it's going to be hard for the next few months," wrote Negredo in a post accompanied by a picture of his right foot in a protective boot.
"I fractured my fifth metatarsal and will be out a few months.
"I will be back stronger than ever."
Negredo endured a season of two halves in his debut campaign at City following his move from Sevilla last July.
The 28-year-old hit the ground running superbly for the Premier League champions, scoring 23 times in all competitions by late January.
However, a shoulder injury sustained in a League Cup tie at West Ham disrupted his flow, with his last goals of the season coming in that match at Upton Park on January 21.
Negredo's under-par second half of the campaign cost him a place in Spain's World Cup squad, and his hopes of repeating his blistering start in 2014-15 have been dashed by this latest injury blow.
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