The ministry also said in a statement that the International Association of Athletics Federations has agreed to allow the 18-year-old Semenya to keep her prize money.
"Whatever scientific tests were conducted legally within the IAAF regulations will be treated as a confidential matter between patient and doctor," the sports ministry said. "As such there will be no public announcement of what the panel of scientists has found. We urge all South Africans and other people to respect this professional ethical and moral way of doing things."
On Wednesday, the IAAF said the gender tests performed on Semenya had not yet been completed. The body had been expected to announce its findings Friday.
Before the 800 final in Berlin, the IAAF said it had ordered gender tests because of Semenya's muscular build and rapid improvement in times. The case set off a storm in South Africa, and the IAAF was accused of violating her privacy. South African track officials were accused of failing to protect her.
Australian newspapers said in September that Semenya has male and female sexual organs, but the IAAF has refused to confirm or deny those reports.
After Athletics South Africa president Leonard Chuene admitted he lied about tests being conducted before the worlds, South African Olympic committee officials suspended him and the rest of the track body's 12-member board.
The Olympic committee appointed one of its members, Ray Mali, as ASA's administrator. When Mali moved into the track body's Johannesburg offices this week, one suspended ASA official had to be escorted from the premises by police.
The sports ministry said Thursday it had asked the IAAF to apologize for its role, and had received this response: "It is deeply regrettable that information of a confidential nature entered the public domain."
The IAAF also told the sports ministry it was not the source of leaks about the case.