Defence Minister Lindiwe Sisulu has accepted the resignation of Defence Secretary Mpumi Mpofu but is still considering that of air force boss Carlo Gagiano, the weekly Mail & Guardian said.
"They have handed their resignation letters," department of defence spokesman Siphiwe Dlamini was quoted as saying by Business Day.
"I am not privy to the contents of those letters. I know the minister (Defence Minister Lindiwe Sisulu ) is considering Mr Gagiano's resignation letter."
The resignations come after a string of incidents involving the transport of Deputy President Kgalema Motlanthe.
Both of them offered to quit over the diplomatically embarrassing incident in which mechanical problems grounded the air force-operated Bombardier plane that was to take Deputy President Kgalema Motlanthe to an official visit to Finland last month, the paper said.
In 2009, on his way back from an African Union summit in Libya, Kgalema Motlanthe's airplane made an emergency landing on a dark runway in the Democratic Republic of Congo after it had missed a fuel stop in the Central African Republic.
In September, the airplane flying him to the opening of the Rugby World Cup in New Zealand missed its first landing slot "as a precautionary measure", according to the defence department.
It conceded in a statement at the time that the aircraft missed the slot because of a "faulty warning light", which suggested there might have been something wrong with the airplane's brakes or tyres.
The aircraft that failed to fly Motlanthe to Finland last month -- a Bombardier Global Express jet -- is the same one that caused panic in New Zealand.
Mpofu resigned last week under pressure from Minister of Defence and Military Veterans Lindiwe Sisulu, who is demanding answers about the chronic mechanical problems of Motlanthe's aircraft. In addition to Mpofu's resignation the chief of the South African Air Force, Lieutenant General Carlo Gagiano, has tendered his resignation, but Sisulu is yet to accept it.
Mpofu refused to respond to the M&G's questions because of the "sensitivity of the matter". "Kindly refer all queries to my former employer," she said.
Sisulu's spokesperson, Ndivhuwo Mabaya, confirmed that Mpofu had resigned "with immediate effect", but denied she had left because of the Finland incident, calling the suggestion "speculative".