The announcement comes as authorities express concern about youths in the Muslim-majority country being radicalised and recruited to fight in hotspots such as Syria.
Police said the five wanted men, believed to be in the southern Philippines, included an Islamic studies lecturer and a stationary shop owner at Universiti Malaya, one of the country's biggest universities.
Three of the men are suspected to be involved in recruiting and sending militants to the group Islamic State of Iraq and the Levant (ISIL), which has seized parts of Iraq and Syria, police said in a statement.
They released photos of the suspects.
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Universiti Malaya said in a statement that the 36-year-old lecturer, Mahmud Ahmad, had been absent and could not be contacted for four weeks, vowing "full cooperation" with the police.
Malaysian police have arrested more than a dozen people in recent months suspected of involvement in Islamic militant activities and intending to send fighters to war-torn Syria.
At least one of them is suspected to have received armed training at a camp run by the Al-Qaeda-linked Abu Sayyaf in the Philippines but managed to sneak back into Malaysia.
But it has been home to several suspected key figures in militant Islamic groups.
In neighbouring Muslim-majority Indonesia, dozens are also believed to have joined the procession of jihadists to Syria and Iraq, sparking fears they will revive sophisticated militant networks when they return and undermine a decade-long crackdown that has crippled the most dangerous cells.