By Agence France-Presse
National police chief Khalid Abu Bakar tweeted that the men were "deported back to Ankara" Thursday night, despite concerns from rights groups who fear Malaysia was bowing to pressure from Turkey.
Turgay Karaman and Ihsan Aslan were arrested last week under a security law which allows detention without trial for 28 days. Two days later Turkish academic Ismet Ozcelik was also detained -- ostensibly for national security reasons.
"Police investigations showed they were involved in FETO activities and are wanted by Turkey," Khalid said in a separate statement.
Turkish authorities allege last year's coup attempt against Erdogan was masterminded by US-based Muslim cleric Fethullah Gulen and his so-called Fethullah Terror Organisation (FETO).
Khalid said the men's travel documents had been cancelled by Ankara and so they were regarded as illegals immigrants in Malaysia.
But rights groups have said they fear Malaysia may be responding to pressure from Turkey, which has mounted a huge crackdown on perceived opponents since the failed coup.
The UN Human Rights Office for Southeast Asia last week expressed serious concern about the arrests and urged Malaysia to refrain from deporting the men to Turkey.
Erdogan's government has detained or sacked tens of thousands of people under a state of emergency imposed after the attempted power grab.
The crackdown focuses on alleged supporters of Gulen.