Colonel Eyal Karim's appointment was announced on Monday but Israeli media have since highlighted a series of problematic statements, including alleged homophobia.
In 2002, when he was a civilian, Karim was asked about whether Jewish scripture permitted soldiers to rape non-Jewish civilians during wartime.
"Although intercourse with a female gentile is very grave, it was permitted during wartime out of consideration for the soldiers' difficulties," he wrote in an answer on a religious website.
"And since our concern is the success of the collective in war, the Torah permitted (soldiers) to satisfy the evil urge under the conditions it stipulated for the sake of the collective's success."
In 2012, he issued a statement saying the comments were taken out of context and stressing he was totally opposed to rape, arguing his statement was referring to biblical times.
The army has also issued a statement saying that Karim "has never written, said or even thought that an Israeli soldier is permitted to sexually assault a woman in war".
Thousands of women serve in the Israeli military but Karim has also said he is opposed to such a policy as it could damage them and the country "due to loss of modesty."
He also suggested gay people were "sick and disabled" and should undergo medical treatment, while arguing that wounded Palestinian suicide attackers should be killed.
His appointment, which still has to be confirmed by Defence Minister Avigdor Lieberman, has been attacked by lawmakers, women's groups and others in Israel.
Prominent opposition MP Shelly Yachimovich on Wednesday called on the army to scrap the appointment.
She said Karim's "odd and chilling" remarks "did not conform with the values of the country and the army."
Zehava Galon, leader of the small opposition party Meretz, also called for the nomination to be reversed.
Military chief of Staff Gadi Eisenkot, however, stood behind his decision.
In a Wednesday meeting with Eisenkot, Karim stressed he supported the enlistment of women to the army, and that he and the rabbinate would respect any person, "regardless of their religion, race or sexual orientation," a statement from the army read.
Eisenkot said he did not agree with Karim's remarks from the period when he was a civilian, which "do not conform with the army's values."
But the chief of staff said he "stood behind his decision" to appoint Karim as the army's chief rabbi.
Karim, 59, is a former rabbi at the Ateret Cohanim yeshiva, or Jewish seminary, in Jerusalem's Old City.
He served in the army and was commander of an elite paratroop brigade.
He is due to succeed Rafi Peretz, who completed a six-year term.
Colonel Eyal Karim's appointment has been attacked by lawmakers, women's groups and others in Israel.
The Israeli army on Wednesday stood by its choice for the next military chief rabbi, after a public outcry over his response to a question on the rape of non-Jewish women in war.
