Government Pathologist Johansen Oduor is overseeing the procedure that seeks to unravel the puzzle of the minister’s sudden death on Saturday morning.
Present at Lee are family members, government officials and Director of Medical Services Jackson Kioko.
Sources told the Nation that Mr Nkaissery’s family had appointed a pathologist, who is expected to work with Dr Oduor during the autopsy.
The surgical procedure had been planned to take place Sunday but was postponed to today as the family awaited the return of one of Mr Nkaissery’s sons from the US, according to sources.
He arrived on Sunday afternoon.
The autopsy is part of the broad investigations the government has launched to establish the cause of the CS’s death.
Sources close to the investigations told the Nation they were pursuing three possible causes: poisoning, a heart attack and an embolism, a blocked artery caused by a foreign body.
They include waiters who served him at the Bomas of Kenya bar and police bodyguards who had been assigned to him.
Director of Criminal Investigations Ndegwa Muhoro on Sunday said the post-mortem is key to the investigation.
“We are looking into it (death) but the post-mortem will determine the direction of the investigations,” Mr Muhoro said.
“The law requires that sudden death must be investigated.”
It is not clear when the autopsy results will be out and if they will be shared with the public.