The move comes as previously friendly relations between Kuala Lumpur and Pyongyang have been badly strained by the killing with a nerve agent of North Korean leader Kim Jong- Un's half brother at a Malaysian airport on February 13.
The Malaysian companies -- 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.
Police cited media reports saying Glocom does not actually exist in Malaysia, and its website glocom.Com.My has been shut down.
The Malaysian companies connected to Glocom, which are said to be controlled by North Korean shareholders and directors, would be "struck off" the list of registered companies, police chief Khalid Abu Bakar said.
Police cited reports saying International Global System registered glocom.Com.My in 2009 while International Golden Services was said to have been listed as the contact point on the website.
"We have also taken all necessary actions to comply with international regulations with regards to related sanctions," he added.
The move from Malaysia came after the UN Security Council on Monday unanimously condemned Pyongyang for its "irresponsible and provocative" attempts to evade restrictions.
The Security Council has imposed six sets of sanctions on North Korea -- two of which were adopted last year to significantly ramp up measures and deny Jong-Un's regime hard currency revenue.
China, Pyongyang's main trading partner, has suspended all imports of coal from North Korea for the remainder of the year to shore up its compliance with the sanctions resolution.
Britain on Monday urged Malaysia to share evidence from the VX attack with the United Nations, which could take action against North Korea.
South Korea has blamed the Pyongyang regime for the murder and slammed the use of the toxin as a "blatant violation of the Chemical Weapons Convention and other international norms".
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