Police arrested 10 Malaysians earlier in the week during raids in and around the capital Kuala Lumpur and the northern state of Kedah before a man attempting to flee the country was detained on Thursday, said a Home Ministry official.
"Our biggest worry is organisations using humanitarian missions as the basis to train militants," said Home Minister Zahid Hamidi as cited by Malay-language daily Berita Harian in comments confirmed by the official.
Hamidi said these groups claimed to be on a "jihad (holy war)", according to the newspaper Utusan Malaysia.
Malaysia practises moderate Islam and has not seen any notable terror attacks in recent memory, but concern has risen in the multi-faith nation over perceived Islamisation.
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Police have said they are also probing terrorism as one possible reason for the March 8 disappearance of Malaysia Airlines flight MH370.
A source familiar with the arrests told AFP on Monday that those detained were not linked to Jemaah Islamiyah or the disappearance of the jet.