The three were detained yesterday at the Kuala Lumpur international airport while waiting for a flight to Turkey, said Ayob Khan Mydin Pitchay, who heads the national police counter-terrorism unit.
"From Turkey, the men were planning to make their way to Syria to join the Islamic State terror group," Ayob Khan said.
He said police believed the men an architect and a technician, both aged 26, and a 46-year-old shopkeeper were recruited through Facebook and other social media sites and were in contact with Malaysians fighting in Syria.
Ayob Khan said authorities have identified at least 22 Malaysians fighting in Syria, including three men who had died.
He said police are still hunting for five suspected militants, including a former lecturer and a sundry shop owner who are believed to be leaders of a local militant group that is recruiting, training and sending Malaysians to fight in Syria and Iraq.
Malaysian authorities earlier this year detained 19 suspected militants for allegedly planning to carry out terrorist acts in the country and abroad. Seven have been charged so far and the rest released.