Siti Aisyah and Doan Thi Huong both said they were not guilty in the killing of Kim Jong Nam, who died suddenly February 13 in Malaysia.
Police said they killed Kim by smearing VX, a deadly nerve agent, on his face while he was waiting to catch a flight at Kuala Lumpur International Airport.
If found guilty, they will face the death penalty, according to charge sheets read in court Wednesday. The women have not entered formal pleas, which will take place when the case reaches the High Court.
Wearing a red T-shirt and appearing to be on the verge of tears, Aisyah, an Indonesian citizen, was led to the dock in handcuffs.
"I do not admit this," she said when an interpreter asked her whether she understood the charges, before repeating, "I am not guilty of this."
Huong, a Vietnamese who was photographed after the crime wearing a sweatshirt emblazoned with the letters "LOL," also said she was "not guilty" of murder.
The charge sheet also mentioned "four others at large" who took part in the crime. Malaysian officials have previously named four North Koreans as suspects, with another three wanted for questioning.
Suspect thought she was using baby oil
Aisyah thought the substance she rubbed on Kim's face was "a kind of oil, baby oil, something like that," said Andreano Erwin, Indonesia's deputy ambassador to Malaysia.
After the women wiped Kim's face with the liquid, he started feeling dizzy and died shortly afterward on his way to the hospital, Malaysian police said.
"And now the person next to me will become a (celebrity)," one friend is heard saying in the video, prompting Aisyah to laugh.
"It would be impossible for such a tiny person like her to do such a crime if she was not manipulated," she said.
A friend who spoke to CNN on condition of anonymity agreed, saying that Aisyah was "naive" and easily "manipulated."
"Whatever that people said, she would believe. She would only follow," the friend said.
Erwin, the Indonesian diplomat, said outside court Wednesday that he had met with Aisyah and she was "not alone."
"Indonesia will always be with her," he said.
North Korea calls allegations 'smear campaign'
"The assassination of Kim Jong Nam was an act of systematic terror ordered by Kim Jong Un," South Korean lawmaker Kim Byung-kee said in a televised address. "The operation was conducted with two assassination groups and one supporting group."
But North Korea furiously denied the allegations in an article posted Wednesday by the state-run Korean Central News Agency.
"The US and South Korean authorities are groundlessly blaming the DPRK ...," the article said, using the acronym for the Democratic People's Republic of Korea. "Almost all countries have scrapped chemical weapons under the convention on ban on chemical weapons but only the US and some other countries still possess (them)," the article said.
North Korea also suggested the United States had given the nerve agent to South Korea and accused both countries of starting a "anti-DPRK smear campaign."
"The US and its vassal forces should not run amuck, clearly understanding the strategic position of the DPRK as a nuclear power," the article said.
Journalist Sandi Sidhu and CNN's Pamela Boykoff reported from Kuala Lumpur, and CNN's James Griffiths wrote from Hong Kong. Journalists Salhan Ahmad and Yoonjung Seo contributed to this report.