"Selamat Triggal Malaysia! After a productive multilateral & bilateral visit, PM @narendramodi emplanes for Sinapore," external affairs ministry spokesman Vikas Swarup tweeted.
"Later today, the PM will deliver the Singapore Lecture on 'India's Singapore Story' at 1730 Indian Standard Time," Swarup added.
Earlier on Monday, Modi held bilateral talks with Malaysian Prime Minister Najib Razak, following which a joint statement was issued by the two countries.
Modi and Razak also jointly inaugurated a Torana Gate, a traditional gateway to Hindu and Buddhist temples, at Bricksfield locality in Kuala Lumpur, also known as Little India.
Later in the day, the Indian prime minister held a meeting with corporate Malaysia.
Modi, who arrived in Kuala Lumpur on Saturday, attended the 13th Asean (Association of Southeast Asian Nations)-India Summit and the 10th East Asia Summit.
He also held bilateral meetings with Chinese Premier Li Keqiang and Japanese Prime Minister Shinzo Abe on the sidelines of the summits.