The soldiers said that he told them they were shaming the country by putting up the pride flag. The young men, who train several months a year at the southern base where the incident occurred, refused to take down the LGBT symbol, which remains on display in their room.
The IDF confirmed the details but said that the incident was not intended to hurt the soldiers, but to "keep up the appearance of the base."
The group of soldiers was received at the Homefront Command base in recent days; the soldiers were assigned rooms and hung their personal items up on the walls.
During the initial inspection conducted on Tuesday by the base's master sergeant, a young staff sergeant who extended his time in the IDF beyond the mandatory service, the master sergeant noticed a LGBT flag with a Star of David in its center, and ordered its removal, according to the soldiers.
In conversations with relatives, the Nahal soldiers claimed that the ban placed by the master sergeant and his disrespectful and angry tones was what offended them.
A source familiar with the soldiers said "they were hurt and had a hard time understanding what bothered him about this flag. But eventually they received the support of a number of the commanders in their company."
At this stage it remains to be seen whether the order would be enforced and the flag removed. There is no ban in the IDF on hanging LGBT flags in private spaces like bedrooms – as opposed to public spaces on base, where only national flags and company flags may be hung.
In their own bedrooms, soldiers are prone to hanging a variety of flags, including those that symbol their seniority in the service and flags of assorted sports teams.
In the 24 hours since the story first broke out, the Homefront Command, that is responsible for the base, held discussions with commanders in the Nahal Brigade on the incident.
An officer in the Nahal Brigade criticized the master sergeant, telling Ynet: "His behavior was unacceptable and the soldiers made sure to hang the flag - that wasn't very big as it is - inside the room, where the sleep. It's not like the flag was put in the center of the company or the base."
The officer added that quite a few gay soldiers want to serve in the Nahal Brigade, and specifically in the 50th Battalion, because of the liberal and accepting nature of those who serve in it.
The IDF is considered one of the more liberal armies in the Western world as far as LGBT soldiers' human rights are concerned.
In recent months, an officer from the Education Corps started giving lectures about the history and rights of the LGBT community to soldiers in Education Corps courses. These lectures are this officer's own initiative.
Despite that, these lecturers are not given in commanders' courses, or at the IDF's officers school. This leads to a situation in which a combat officers coming from a conservative background might have a hard time helping a soldier under his commander that turns to him with a problem that derives of his sexual orientation.
In addition to that, in the past two years the Advisor to the Chief of Staff on Women's Issues formed an experts' committee that convenes whenever necessary to aide transgender soldiers serving in the army on a one-on-one basis.
"The IDF was quick to brand itself as a liberal army after releasing a story of two male soldiers walking hand in hand on the street last year. The picture was good for the army's public relations, but it still has a long way to go on the issue," a lesbian officer who served in the combat Caracal Battalion told Ynet.
"It doesn't make sense that in many training bases and outposts of combat units, commanders will say things like 'what are you, gay?' to their soldiers, or ignore such comments when they are made. These comments are made in front of a division of 30 soldiers, some of which could be in the closet. The army has to invest in education on the topic, especially in combat units," she continued.
Daniel, who served in the same base as the Nahal Brigade where the incident took place, claimed that 30% of the soldiers from the 50th Battalion in the base are out of the closet.
"Commanders' treatment of them is generally good and reasonable. Last year there was a case when soldiers were not allowed to leave the base to attend the pride parade, but as an alternative commanders organized a small pride parade in the base, alongside conversations and activities that have to do with the LGBT community," he said.
The IDF Spokesperson's Unit said on Wednesday that the "incident was taken out of context. The order was given the soldiers with the intention of maintaining the appearance of the base and not out of malicious intent."