Two transgender people were packed in sacks, thrashed with sticks and tortured to death, according to human rights activists.
Police allegedly killed 35-year-old Amna, and Meeno, 26, both Pakistanis, after raiding a house in Saudi Arabia and arresting 35 transgender people.
Activists in Pakistan are demanding clarification from Saudi Arabia over the deaths and the 22 people reportedly still in custody.
“We want information because right now this is a very confusing situation and many in the transgender community in Saudi Arabia are feeling delicate and scared,” said Qamar Naseem, a feminism and social rights activist from the Blue Veins group, speaking to The Independent.
“They are not treated fairly even by criminal law in Saudi Arabia, and it’s not just people from Pakistan, it’s people from different parts of the world.
“Gender fluid people are treated badly, sometimes flogged, and if someone is arrested on the same law for a second time they can be executed.”
Mr Naseem said he and TransAction Pakistan president Farzana Jan were told by a transgender contact in Saudi Arabia about the raid.
They were allegedly arrested for cross-dressing and for having same-sex relationships in the capital of Riyadh.
Homosexuality is punishable by death while any sex-change surgery is illegal.
Mr Qamar said the group were hosting a Guru Chela Chalan gathering, a Pakistani ceremony celebrated in the transgender community, in which they choose their 'guru' leader.
Eleven were reportedly arrested after paying a 150,000 riyals fine (£33,000) while 22 were kept in custody.
He said the two victims, from Khyber-Pakhtunkhwa in Parkistan, were “kicked and beaten in bags”.
The Travel Agents Association of Pakistan was reportedly told last year not to grant visas to transgender people planning the Hajj or Umrah pilgrimage.
Saudi Arabia last year insisted the United Nations keeps LGBT rights out of its development goals.
"Amnesty International has been unable to verify this information, but urges the Saudi Arabian authorities to comply with their duty to conduct a thorough and independent investigation into any allegation of torture and extra-judicial executions and bring those suspected of criminal responsibility, including state agents, before ordinary courts in proceedings that meet international standards of fair trial and without the recourse to the death penalty," said an Amnesty International spokesman.
"The authorities must diligently investigate any possible discriminatory motive in these crimes, including discrimination on the basis of gender identity and expression."
The Independent has contacted the House of Saud and Pakistan’s Ministry of Human Rights for further comment.