The foreign affairs minister, Penny Wong, says she believes the Australian women who have alleged they were sexually assaulted and beaten by Israeli soldiers after being detained as part of a humanitarian flotilla attempting to bring aid to Gaza.

Appearing at Senate estimates, Wong said the treatment of the Australian women was “unacceptable”, and the allegations they had subsequently made were “distressing”.

“My principled position is to always believe women when allegations of sexual assault are made,” Wong said.

Eleven Australians were part of the Global Sumud Flotilla, sailing from Mediterranean ports in an attempt to deliver food, medicine and baby formula to the war-ravaged Gaza Strip, blockaded by Israel.

The boats were intercepted by Israeli naval forces and those onboard – unarmed civilians – were detained and deported, with some alleging violent abuse including beatings and rape. Israel has denied the allegations.

Wong told the estimates committee: “Those allegations are terrible. They are horrific. The treatment is unacceptable. And I express my empathy to those women to whom that was done.”

She said the Australian government had raised concerns with Israel over the treatment of flotilla sailors, and Israel’s refusal to grant Australian diplomats access to the Australians detained.

The Greens senator Mehreen Faruqi detailed allegations made by some of the Australians detained by Israel.

“One of these flotilla participants, Juliet Lamont, has said she was sexually assaulted and beaten, cable tied and had so much water thrown in her face that at one point she thought she was going to drown. She says ‘they wrenched my trousers and underwear down and I was raped by one of the soldiers’. My daughter was syringed with an unknown substance. Other people had guns inserted inside them.

“Neve O’Connor, another one of these brave humanitarians, has said she was abused, physically beaten and sexually humiliated. She says ‘I had my hands pinned behind my back while being repeatedly kneed in the spine, kneed in the thighs’.

“And Violet CoCo has told us that she was held at gunpoint, stripped of her clothes and pushed into a shipping container where she was beaten, kicked and sexually assaulted before being thrown into a prison yard.”

Faruqi asked Wong directly: “Do you believe these women?”

Wong responded: “My principled position is to always believe women when allegations of sexual assault are made.”

In a heated exchange with Faruqi, Wong reasserted her position: “You should believe, and I believe, women who come forward with these assertions.”

The Senate committee broke before later returning to the subject.

In the latter debate, Wong confirmed her office was in direct contact with some of the Australian women who had been part of the flotilla.

“My view is that … women should be believed in these allegations, which are confronting and distressing, should be dealt with respectfully and seriously, and that is what we will do: I don’t intend, in this forum, to go into these issues any further.”

Three members of the flotilla – including Lamont – held a press conference at parliament house on Thursday, asking for a meeting with the foreign and prime ministers.

“I’m really glad that Penny [Wong] recently said that she believes us,” Lamont said.

“I think the extension of that is she needs to meet with us, she needs to hear our testimony and she needs to sanction Israel. What other country would be allowed to rape and torture 11 ordinary citizens from this country and get away from it?”

The Israeli embassy in Australia issued a statement last week saying the flotilla was “organised for provocation rather than humanitarian concern”, and alleging some on board were “well-known agitators”.

“The provocateurs were neither tortured nor raped. Such claims are entirely baseless and are intended solely to advance the provocateurs’ smear campaign against Israel.”

Wong was also asked at Senate estimates about Australia’s broader relationship with Israel. She rejected the assertion she had described Israel as an “ally”.

“That is not a phrase I use because we don’t have an alliance. We have alliance partners.”

Wong said Australia was currently experiencing “one of the most challenging times” in the history of its relationship with Israel.

“Australia is strongly opposed to many of the actions of the Netanyahu government and we have been clear about that opposition.

“Mr Netanyahu, and some of his colleagues, have had plenty to say about our government, and about Australia.”

Wong said Australia had raised with Israel concerns about violence in Gaza and illegal settlements in the West Bank. She condemned the lack of progress in investigations into the death of the Australian aid worker Zomi Frankcom and her colleagues, who were killed by the IDF.

Wong also decried the refusal to allow Australian diplomats to undertake work in Palestine, the damage to Australian veterans’ war graves in Gaza and the alleged mistreatment of Australian citizens.

“Now, this is a pattern of behaviour, which makes it difficult to … unless the pattern of behaviour changes, it is very difficult to see the relationship changing.”