"Zaheer Khan has been ruled out of the forthcoming Sri Lanka series because of a shoulder injury. The All-India Senior Selection Committee has chosen Abhimanyu Mithun to replace him," Board Secretary N Srinivasan said in a BCCI release.
The BCCI did not divulge any details of the injury. It also did not mention for how long he has been adviced to rest.
It was also not clear whether he will miss the ODI tri-series starting on August 10 at Dambulla, also featuring New Zealand, though its squad will be announced later.
Zaheer was rested for the recent tour of Zimbabwe in order to keep him fresh for the busy season ahead. He played in all of India's matches in the recent Asia Cup at Dambulla.
Uncapped so far in Test, Mithun was included in the Indian squad for the two-Test series against South Africa early this year but did not play any match.
The Karnataka speedster played an ODI against South Africa in Ahmedabad, in February this year.
The lanky pacer was withdrawn from the India A squad in England to replace injured seamer Vinay Kumar in Zimbabwe, but didn't get a game. He rejoined his team-mates in England for the one-dayers and in his most recent outing on Friday, took 3 for 49 against West Indies A.
India begin their tour of Sri Lanka with a three-day game against a Sri Lankan side in Colombo from June 13-15 before the first Test in Galle from July 18.
The second Test starts in Colombo from July 26 while the third and final Test will also be played in Colombo from August 3-7.