Nine Israeli soldiers detained on suspicion of abusing a Palestinian prisoner are facing charges of sexual assault, it has transpired.

The soldiers were arrested on Monday at the Sde Teiman detention centre in the Negev desert.

Dozens of hard-Right activists stormed the Israel Defence Forces (IDF) base in protest at the soldiers’ arrest, sparking a furious political row and criticism from the IDF’s chief of staff.

On Monday evening, hundreds of ultra-nationalists stormed the Beit Lid military base, where the detained soldiers had been transferred.

On Tuesday, a defence lawyer for three of the arrested soldiers said they were facing charges for “acts of sodomy”.

The Haaretz newspaper reported that the inmate had suffered injuries to an intimate body part “which left him unable to walk”.

Nati Rom, the defence lawyer, told the Associated Press that the inmate was a high-ranking Hamas member who had attacked some of the officers. He denied they had done “anything sexual” to him.

Orit Sulitzeanu, the head of the Association of Rape Crisis Centres in Israel, said she was “shocked” to hear of the allegation.

“There are never any circumstances to justify the use of this sickening practice, not even against the worst of our enemies. Sexual harm and sexual abuse are serious crimes and we must not remain silent when they happen,” she told Haaretz.

The nine soldiers were due to appear for a hearing at a military court on Tuesday.

Isaac Herzog, the president of Israel, called for an “immediate, in-depth, sensitive and responsible investigation into the allegations” of abuse against the Palestinian detainee.

The riots and illegal storming of both military sites on Monday divided Israeli lawmakers within the government of Benjamin Netanyahu, the prime minister, who issued a short statement in which he condemned the incident and called for “immediate calm”.

Herzl Halevi, the chief of the IDF, declared the forced entry into military bases “serious, unlawful behaviours bordering on anarchy, harming the IDF, the security of the state, and the war effort”.

Yair Lapid, the leader of the opposition, called it “an attempted coup by an armed militia”.

But other ministers and coalition lawmakers defended and even took part in the riots. Itamar Ben-Gvir, the national security minister, supported the storming of the sites, while at least one member of the Jewish Power party, Amihai Ben-Eliyahu, the minister of heritage, joined the break-in of the Sde Teiman facility.

Tally Gotliv, a lawmaker from Mr Netanyahu’s Likud party, also showed up at the site, appearing next to armed and masked activists. “No one will determine for us what is right and what is not in protests,” she later said.

In May, CNN reported that Palestinians arrested in Gaza had been facing brutal conditions at the camp, some of whom had been blindfolded and beaten.

A New York Times investigation also found that about 1,200 Palestinian civilians had been held at the camp “without the ability to plead their cases to a judge for up to 75 days”. The prisoners can also be denied access to a lawyer for up to 90 days.

Seven inmates told The New York Times they had been forced to wear nappies while being interrogated. Three said they had received electric shocks.

The Israeli government announced last month that it would begin reducing the number of inmates held at the camp.