Peretz summoned Raved to what IDF sources called a "harsh hearing" following his decision to leave the program. Following the hearing, Peretz decided to recommend that Raved be dismissed from the military immediately.
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Raved's service was due to end in the summer of 2012. Peretz' recommendation has been forwarded to the head of the IAF Personnel Directorate Brigadier-General Ilan Boger.
Raved's Tuesday resignation from the program came a day after the army announced it would not excuse religious soldiers from official events that feature female soldiers singing.
The IDF said that the recruitment program, known as Shahar, would not be affected by Raved's decision.
An army official slammed the resignation as "a coordinated move by elements within the ultra-Orthodox community," but added that the military did not intend to take any disciplinary action against the rabbi, given the proximity of his retirement from service.
"I participated in formulating the guidelines which inspired the Shahar Program," Raved wrote in his letter of resignation.
"I was guided by the need to allow haredi soldiers to maintain their way of life and observance. Over the past few months, the (IDF) Personnel Directorate had decided to review these guidelines. I was part of those deliberation and saw how the last draft excluded sections meant to maintain the soldiers' observance and included sections that may infringe on that."
The IDF said: "The Shahar Program is part of the national effort made to ensure members of all Israeli society serve in the IDF, including haredim. The past few years have seen a significant growth in haredim's service and the IDF lends that great importance.
"Following the conduct of the IAF rabbi, the chief military rabbi saw fit to summon him for a hearing, and then forwarded his recommendations to the rabbi's superior officers in the IAF."
Yoav Zitun contributed to this report
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