Ahmad Zahid told a news conference that Malaysian airport and border security had been increased, while illegal routes commonly used by smugglers were being monitored.
Malaysia has been exchanging intel with international intelligence agencies, and has a suspect list which includes names of those believed to have ties with Islamic State (IS), he said.
According to the police’s figures released last month, 90 Malaysians have joined IS in Syria and Iraq since 2013.
In August, Malaysia revoked the passports of 68 Malaysians who had been identified as leaving the country to join IS.
Returning fighters would be detained and sent for deradicalisation, Ahmad Zahid said.
A total of 137 people have been arrested for either planning to join IS overseas, returning to Malaysia after joining the group, or sending funds to the group, he added.
Defence Minister Hishammuddin Hussein said on October 17 that intelligence sources suggested that thousands of IS members would make their way back to their countries of origin, or find safe havens in regions such as Southeast Asia, if the Mosul offensive succeeds.
Malaysia has been on high alert since IS-linked militants carried out an armed attack in the capital of neighbouring Indonesia in January.
In June, eight people were injured when two IS supporters threw a grenade into a bar on the outskirts of Kuala Lumpur, the first successful attack by the group in the Malaysia.