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Indian Prime Minister Narendra Modi has held talks with new Malaysian leader Mahathir Mohamad in a brief visit aimed at bolstering bilateral ties.

He flew in from Indonesia for the second leg of his Southeast Asian tour and met Mahathir on Thursday at the government administrative capital of Putrajaya.

Modi tweeted: "I thank him for the warm welcome. We had productive discussions on further cementing India-Malaysia ties."

His visit was greeted by a small protest at Putrajaya by ethnic Indians and Muslim groups who chanted "Go back Modi" and carried placards blaming his government for tolerating alleged human rights abuses in India.

Modi was the third foreign leader, after the Singapore premier and Brunei's sultan, to meet Mahathir since his alliance's stunning victory in May 9 national polls.