Police have been accused of killing 26-year-old Meeno and Amna, 35, after raiding a house party in Saudi Arabia and arresting 35 transgender people.
Saudi media reported police raided a party where men were dressed as women and wearing make-up but did not use the word transgender.
A statement from the Saudi interior ministry said the reports accusing of police of beating two Pakistanis to death were “totally wrong and nobody was tortured”.
He added: “One 61-year-old person suffered a heart attack and died in the hospital after being treated.
“The Pakistani embassy looked into this case and another one. Procedures have started to send the body back to his country.”
The arrests were allegedly made for having same-sex relationships and for cross-dressing in the Saudi Arabian capital Riyadh. Homosexuality is punishable by death while any sex-change surgery is illegal.
Farzan Riaz, a leader of the group Trans Action Pakistan, claims the two Pakistanis were beaten to death with sticks after being “kicked and beaten in bags”.
She added: “We are deeply saddened by the deaths of these two innocent trans persons in Saudi Arabia.
“We request the Saudi government to release the information of the 35 transgender persons arrested; we want to know their details, under what charges were they arrested, what is their medical condition?”
Qamar Naseem, a rights activist from the Blue Veins group, said the “gender fluid” group are victimised in Saudi Arabia and “not treated fairly even by criminal law” while “if someone is arrested on the same law for a second time they can be executed.”
In Pakistan, transgender people are often shunned by their families and forced into begging or prostitution to support themselves.