The estranged half-brother of the North Korean leader would have died "in a very short period of time", Health Minister S. Subramaniam added.
Malaysia revealed Friday that the 45-year-old victim was killed with the VX nerve agent, which is so deadly it is listed by the UN as a weapon of mass destruction.
Police are holding two women suspected of staging the attack as well as a North Korean man.
They want to speak to seven other North Koreans including a senior embassy official, but four of the suspects fled Malaysia on the day of the murder.
The two women can be seen shoving something into Kim's face in leaked CCTV airport footage of the brazen February 13 attack. He later suffered a seizure and was dead before he reached hospital.
Nerve agents prevent the proper operation of an enzyme that acts as the body's "off switch" for glands and muscles.
Without that switch, glands and muscles are constantly being stimulated, eventually tire and become unable to sustain breathing.
Subramaniam told reporters the cause of death was now "more or less confirmed".
The scene of the killing, the budget terminal of Kuala Lumpur International Airport, was swept by civil defence personnel in hazmat suits overnight before being declared safe.
Police sealed off large areas of the Terminal Two departures hall as a few curious onlookers watched.
"The police cordon was at three areas -- the scene of the attack, the bathroom where the two female suspects washed their hands and pathway leading to the airport clinic -- (and) has been taken down," a police spokesman said.
Investigation ongoing
The operation came almost two weeks after Kim's death and puzzled some travellers.
Student Hariz Syafiq, 21, who was due to take a domestic flight later, told AFP: "Yes, I'm worried a bit. Why didn't they quarantine the airport?
"It's a bit strange."
Both women suspected of carrying out the attack insisted they thought they were taking part in a prank video, although Malaysian police have said they knew what they were doing.
One of the two female suspects in custody, 25-year-old Indonesian Siti Aisyah, reportedly told a senior diplomat Saturday she had been paid just 400 ringgit ($90) for her role, adding she believed she was handling a liquid like "baby oil".
The other woman, Vietnamese Doan Thi Huong, 28, told Hanoi officials she had been tricked into killing Kim and thought she was taking part in a prank for a comedy video.
Indonesia's deputy ambassador to Malaysia Andreano Erwin, who was granted consular access to Siti Saturday, reportedly said she did not know Huong.
Police have said one of the women arrested after the attack fell ill in custody, adding she had been vomiting.
However, Erwin said Siti was physically healthy while Vietnamese officials said Huong was "in stable health".
Selangor state police chief Abdul Samah Mat told reporters an investigation was continuing at an apartment complex in Kuala Lumpur in connection with the four North Koreans who fled Malaysia on the day of the killing.
He added that samples from the address had been sent for chemical analysis.
One man wanted for questioning and believed still in Malaysia is senior North Korean embassy official Hyon Kwang Song, who enjoys diplomatic immunity.
The news Friday that lethal VX nerve agent was used in the attack sparked anger in Malaysia and brought condemnation from South Korea, which has pointed the finger at the North over Kim's death.
Seoul slammed the use of the toxin as a "blatant violation of the Chemical Weapons Convention and other international norms".
No next-of-kin have yet come forward to formally identify the body or provide a DNA sample, but authorities have said relatives would be given more time to do so.
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