The conference focused on clarifying orders aimed at preventing incidents of discrimination against women in the Israeli army.
One the other hand, he added, "it's absurd that there are many religious soldiers in the army, and more and more haredim are expected to enlist while there is no consideration in cases of non-operational or unofficial events.
"If the army fails to consider their feelings, it will be an excellent excuse for the extreme elements which are calling on the ultra-Orthodox not to join the military."
Another rabbi said that "just like soldiers consult me sometimes about questions and answers, the commanders always try to reach a compromise as well. In any case, a commander's order always comes before my recommendation to a soldier."
'No Beit Shemesh-style acts in IDF'
The chief military rabbi declared Thursday that he would prevent any attempt to introduce radical religious beliefs which discriminate against women into the IDF.
In a letter addressed to IDF commanders, Peretz pledged that there would be no Beit Shemesh-style wrongdoings in the IDF. "The spirit of Jewish Law does not allow discrimination against women under any circumstance, of any nature, and any other interpretation which encourages this is wrong.
"We have recently been witnessing a grave phenomenon in which women are being discriminated against outside the army and unfortunately there have also been similar instances inside the IDF," Peretz wrote.
"I find it hard to stand by in the face of such grave incidents. They are immoral, are not in line with the IDF spirit and values and in complete contradiction to the spirit of Judaism."
He further added, "In the IDF, army orders alone dictate the nature of the organization and determine what needs to be done in various cases. I, as chief military rabbi, am working for a common path between the military command system and the halachic value system and a common campaign of all IDF soldiers to prevent any case of discrimination against women in the name of religion within the army."
The IDF chief of staff also referred to discrimination against women over the weekend, saying that "there is no exclusion of women in the IDF, period. It just does not exist."
Gantz noted that the public discussion on women's exclusion in the IDF was more talk than facts.
He added, "The IDF as an organization is not aimed at promoting equality for women, though I am very much in favor of that, it is an operational organization."
Kobi Nahshoni contributed to this report