This new appointment was seen as a direct consequence of the controversial remarks by Israel Weiss wherein he appeared to have agreed with the former Chief Ashkenazi National Authority of Religious Services Rabbi, Avraham Shapira, who called on soldiers who are religious Jews to disobey orders to forcefully remove settlers from the Gaza Strip during the Gaza disengagement plan.

[5] According to Israeli left-wing human rights group Yesh Din, during the 2009 Gaza conflict, the military rabbinate distributed a religious booklet that warned against showing mercy to enemies.

[8] It also accuses the material of fostering an atmosphere in which extremist sermons by Yitzhak Ginsburg praising Baruch Goldstein (described as "chauvinist and racist incitement") can be disseminated.

[8] Following a series of inquiries, both in the Knesset and within the IDF, it was determined that the distribution of the alleged booklets took place in a few isolated incidents, by non-military personnel, without proper supervision of Military Rabbinate representatives.

[9] Following this incident, guidelines were set to ensure the authority of both the Military Rabbinate and the Education and Youth Corps within the IDF.

In November 2016, the High Court of Israel delayed the appointment of Eyal Krim as chief military rabbi, demanding that he clarify a number of statements he had made in the past.

Responding to the accusations, Krim said that the Torah permits intercourse with a non-Jewish woman during wartime under certain conditions, but his statements were strictly theoretical and dealt with a specific biblical passage.