South Korea says its isolated neighbour was behind the assassination, and claims the North's agents engaged two outsiders to carry out the murder.
"They will be charged in court under Section 302 (murder) of the penal code," Malaysia's attorney general Mohamed Apandi Ali told AFP by text message, referring to the two suspects.
The women will appear in court on Wednesday. If convicted, they could face death by hanging.
Kim Jong-nam, a well-travelled polyglot who fell out of favour at home after a botched 2001 attempt to get into Japan, died less than 20 minutes after he was set upon at Kuala Lumpur International Airport on February 13.
CCTV footage shows two women approaching him and seemingly pushing something in his face.
Investigators say this was VX, a deadly poison classed as a weapon of mass destruction and banned around the world.
Indonesian Siti Aisyah, 25, reportedly told a senior diplomat on Saturday she had been paid just 400 ringgit ($90) for her role, adding she believed she was handling a liquid like "baby oil".
Her alleged accomplice, Doan Thi Huong, 28, from Vietnam, told Hanoi officials she had been tricked into killing Kim Jong-nam and thought she was taking part in a prank for a comedy video.
Speaking from the rural Vietnamese village of Quan Phuong, Huong's stepmother appealed for a fair trial.
"I think she was set up." Nguyen Thi Vy told AFP. "I don't believe she was brave enough to do such thing."
A third suspect, 46-year-old North Korean man Ri Jong-Chol, is also being held, but Apandi made no mention of whether he would be charged.
North Korea has not acknowledged the identity of the dead man, but has insisted Malaysia hand over the corpse, and says it does not accept the findings of an autopsy.
Pyongyang has repeatedly lashed out at Kuala Lumpur over the investigation into the killing, claiming the Malaysians are playing politics.
Veteran North Korean diplomat Ri Tong Il, deputy envoy to the United Nations, told reporters outside the embassy he was there to discuss "the question of the return of the body of the deceased DPRK citizen".
He added the North Korean delegation would also raise "the question of the release of the DPRK citizen arrested by Malaysian police".
Malaysia has refused to release the body, with police saying they are waiting for next-of-kin to come forward to identify the remains and provide a DNA sample.
Malaysia's previously warm relations with North Korea have deteriorated sharply since the killing.
On Tuesday, Kuala Lumpur said it was shutting down firms linked to a North Korean front company the UN says was selling military equipment.
International Global System and International Golden Services have been connected to Glocom, which a United Nations' report said was based in Malaysia and operated by Pyongyang's intelligence agency.
The UN report said Glocom was selling North Korean-made military communications equipment to Eritrea, with suppliers in China and an office in Singapore.
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