Malaysian chief police Khalid Abu Bakar said on May 3 that Turgay Karaman and Ihsan Aslan were arrested because they threatened the security of Malaysia.
No further details were provided by authorities and the Turkish embassy refused to comment.
Earlier, the local media reported that both men had been abducted.
On May 2, another Turkish national Suheyl Ozcelik lodged a police report saying that he had seen CCTV footage of five men abducting Karaman, a physics teacher, at a Kuala Lumpur car-park.
Ozcelik also said two of his Turkish friends were abducted last year and deported to Turkey.
Phil Robertson, Deputy Asia Director at Human Rights Watch (HRW), said the Malaysian police should grant the two men immediate access to their lawyers and families and give details of how they posed a threat to Malaysia.-VNA