In a statement, Mr Hishammuddin said he had been "closely monitoring" the recent attacks and bombings in neighbouring countries.
"I have instructed the armed forces to improve border control across the country," he said, noting that the incidents took place in three countries that Malaysia shares borders with.
Two additional ships will be deployed to patrol the waters off Sabah, Mr Hishammuddin said. Quick Reaction Force (QRF) personnel will be placed with troops on islands in Sabah waters, and patrols will be increased in areas that have been identified as entry points into the southern Philippines.
An additional company of army infantry will be deployed in Cenderawasih, Lahad Datu to ensure that its coast is secured.
Mr Hishammuddin added that he has been in touch with his counterparts in the countries involved: Delfin Lorenzana Negrillo of the Philippines, Thailand's Prawit Wongsuwan, and Ryamizard Ryacudu in Indonesia.
He said that the Malaysian Armed Forces will continue working closely with the armed forces of the three countries, and that intelligence is being shared as well.