"We will make defence cooperation stronger. Our agreements on cyber security are very important," Modi said at a joint press conference here.
"We will work with renewed vigour to raise momentum of our partnership. We will continue to deepen security cooperation," he added.
Malaysian Prime Minister Najib Razak was also present at the conference.
Earlier, Modi was accorded a ceremonial welcome here as he entered the bilateral phase of his visit to Malaysia, the third day of his visit to this southeast Asian nation.
Modi was greeted with a hug by Razak at Putrajaya, the federal administrative centre of Malaysia, following which he was accorded a guard of honour.
Modi attended the 13th ASEAN (Association of Southeast Asian Nations)-India Summit on Saturday and the 10th East Asia Summit on Sunday.