Seoul said its armed forces were "closely monitoring the North's military for further provocations and maintaining military readiness".
Ambassador Kang Chol failed to present himself at the ministry when summoned and "is expected to leave Malaysia within 48 hours," the statement added.
The statement from Malaysia's Foreign Ministry said it was "greatly concerned" with the use of the toxic chemical and condemned the use of such a chemical weapon under any circumstances.
The Security Council condemned North Korea's "irresponsible and provocative" attempts to evade UN sanctions.
The United States will on Monday claim its seat at the UN Human Rights Council under the new presidency of Donald Trump.
North Korea has a vast chemical weapons stockpile, including VX, of up to 5,000 tonnes, South Korean experts said on Friday.
"Malaysia is obliged to hand his body to the DPRK (North Korea) side as it made an autopsy and forensic examination of it in an illegal and immoral manner", the North's Korean Jurists Commitee said, in comments carried by KCNA.
Council members including China, Pyongyang's main ally, agreed on a US-drafted statement describing the test-firing of the missile as a "grave violation" of UN resolutions.
"I just want everybody to understand and fully know that the United States of America stands behind Japan, its great ally, 100 per cent," Trump said.
During a joint conference with Trump, Abe called on Pyongyang to comply fully with relevant UN Security Council resolutions. Abe called the test "absolutely intolerable".
Lee Hee-Beom, president and CEO of the POCOG, said the "spirit" of the Olympics was peace citing the traditional suspension of wars in Greece.
The coast guard cited the crew as saying the ship was transporting rice from North Korea's port of Nampo on its west coast to the east coast city of Wonsan.
Seoul's defence ministry said the North is believed to have some 50 kilogrammes of weapons-grade plutonium as of the end of 2016 -- enough to make about 10 weapons
But the recent barb trading could suggest Pyongyang and Washington are feeling each other out ahead of President-elect Trump's inauguration on January 20.