The man was not beheaded as had earlier been reported, Lieutenant Colonel Mashay Gamieldien said.
"The cause of death is still being determined by the post mortem."
According to MambaOnline, Shaine Griqua, Director of Legbo Northern Cape, who first reported the attack, said that confusion around the state of the body likely stems from miscommunication due to most people in the area not speaking English as a first language.
It was reported 23-year-old Thapelo Makutle, on Friday became involved in an argument with two heterosexual men about his sexuality.
Gamieldien said Makutle was found in his rented room early on Saturday morning with a wound to the neck.
"No arrests have been made and police are still searching for the suspect or suspects."
He was recently crowned Miss Gay Kuruman and took part in the Kimberley Out In Africa Gay and Lesbian Festival.
Democratic Alliance parliamentary leader Lindiwe Mazibuko said the murder was a reminder that many South Africans were still denied basic rights and freedoms.
She said a number of hate crimes against gays and lesbians, such as corrective rape, had taken place across the country.
President Jacob Zuma should speak about the man's murder and others like it, Mazibuko said.
Zuma's spokesperson Mac Maharaj said the government's record on supporting gender and gay rights was well known, and eliminating discrimination was an on-going process.
"We take any event that does not uphold these rights, that violates these rights, as a blot on our society and it needs to be counteracted at every level in our society," he said.
*In an earlier report it was incorrectly claimed that the victim was beheaded