Prosecutor Iskandar Ahmad gave no explanation for the refusal to drop the murder charge against Doan Thi Huong, who is the only suspect in custody after the stunning decision to drop the case Monday against Indonesian Siti Aisyah.
But no such political decision appears to have been made in the case of Doan Thi Huong, prompting claims of unfairness by her lawyer Hisyam Teh Poh Teik.
"God knows that Siti and I did nothing wrong", Huong told reporters in court through an interpreter, according to the Guardian.
"We expect the government's assistance so that Huong can soon be home".
Indonesia had mounted a sustained diplomatic offensive to get Aisyah freed, while Vietnam had only stepped up pressure since the Indonesian woman's release this week.
Nam was assassinated with a liquid VX nerve agent in February 2017 at Kuala Lumpur airport.
The go-ahead was given by the Malaysian attorney general, the court was informed.
"The decision not to withdraw does not sit well with our criminal justice system".
"[The] AG has not acted fairly".
Both women insist they are innocent. The Guardian reported that Huong looked pale and drawn.
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Doan Thi Huong, 30, has been on trial for a year and a half over the 2017 assassination of Kim Jong Nam at Kuala Lumpur airport that shocked the world. She left after about an hour.
Judge Azmin Ariffin accepted Teh's request and adjourned the case to 9 a.m. on April 1.
"I have no idea what is going on", Huong said in the courtroom Thursday.
Vietnam's ministers of justice and foreign affairs are communicating with their Malaysian counterparts to secure his client's release, Teh added.
Vietnamese Ambassaador Le Quy Quynh said he was "very disappointed" with the attorney general's decision.
Vietnam's foreign ministry expressed "regret" at the outcome while a politician criticised it as "mind-boggling".
Both have insisted they were tricked into the brazen attack and thought it was part of a TV show.
Defence lawyers have maintained the women were pawns in an assassination orchestrated by North Korean agents. An Interpol red notice alert has been placed on the four men.
South Korea accuses Pyongyang of plotting the murder of Kim Jong Un's estranged relative, who was once seen as heir apparent to the North's leadership.
The defense phase of the trial is expected to shift the focus onto the absent North Koreans.
Two other North Korean nationals, whom Malaysian police had identified as persons of interest in the investigation, were on the same commercial flight that carried Kim's body out of Malaysia.