Jon Niese’s season is in jeopardy after Mets doctors yesterday diagnosed the pitcher with a partial tear of the rotator cuff in his left shoulder.

The 26-year-old lefty, who was placed on the disabled list, departed early from his start in Atlanta Thursday night with soreness in the shoulder he believed stemmed from a recent bout of tendinitis. But an MRI exam yesterday at the Hospital for Special Surgery in New York revealed the extent of the injury, according to assistant general manager John Ricco.

Surgery has not been prescribed for Niese, who will rehab with physical therapists for the next two weeks before another MRI is taken to measure any progress.

“According to the doctors, it’s a small enough tear that they are hopeful he won’t need surgery,” Ricco said before the Mets’ 4-3 victory over the Phillies last night at Citizens Bank Park. “It’s not a full-thickness or significant tear at this point.”

Niese, who signed a five-year deal worth $25.5 million with the Mets before the 2012 season, is 3-6 with a 4.32 ERA in 14 appearances this year. He missed a start against the Marlins this month because of tendinitis in the shoulder. Ricco said there was no evidence of a tear in the shoulder when the tendinitis was diagnosed.

Ricco would not speculate on how long Niese might be sidelined other than to say the pitcher will rest for the next two weeks.