He also said that his country would continue to talk about the Kashmir issue "through channels that are acceptable" and prayed that "the issue is amicably resolved".
In a series of tweets, Mahathir Mohamad had said that 'Muslims have a right to be angry and kill millions of French people for the massacres of the past'. It sparked an angry outburst on social media with many users calling out the former Malaysian prime minister.
The 92-year-old, who returned to politics after a decade-and-a-half, ousted Najib Razak.
Naik was booked by the Enforcement Directorate in 2016 based on a National Investigation Agency FIR that was registered under the Unlawful Activities Prevention Act.
Mohamad made some adverse comments against the citizenship law at a press conference in Kuala Lumpur.
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'My aim has always been to foster communal peace and harmony'
Mahathir Mohamad, 77, is credited with putting Malaysia in the front rank of newly industrialized countries.
"Prime Minister Modi raised the issue of Zakir Naik's extradition. Both the parties have decided that our officials will stay in contact regarding the matter and it is an important issue for us," Foreign Secretary Vijay Gokhale said on PM Modi's meeting with Mahathir.
The external affairs ministry on Friday termed as "factually incorrect" remarks reportedly made by Malaysian Prime Minister Mahathir Mohamad's that India is taking action to deprive some Muslims of their citizenship. The ministry also said Malaysia should refrain from commenting on the internal developments of India, especially without a right understanding of the facts.
Mahathir said his govt would always ensure it looked into all factors.
In a media briefing on Tuesday in New Delhi, Foreign Minister S Jaishankar said Naik's extradition issue had indeed come up during prime minister Modi's meeting with Malaysian counterpart in Vladivostok. Jaishankar said India has already placed a request with Malaysia for Naik's extradition in January.
Sharif, the PML-N prime ministerial candidate, said that Pakistan cannot become a great nation by voting leaders like Imran Khan who have made false promises to "our nation".
Modi is among the first world leaders to meet Mahathir, who became the world's oldest elected leader.
Acknowledging the strained diplomatic relations between Malaysia and India over his remarks, Mahathir said that it is necessary to speak out on the issues, even though such remarks could be disliked by some.
'This visit will further the convergence of our political, economic and strategic interests,' Modi tweeted.
Mahathir Mohamad's statement came a day after the ministry of external affairs said that the extradition request of Naik made by India is under the active consideration of the Malaysian government, as per the media reports.
Naik's detractors -- those with 'a mob mentality' -- should debate him rather than asking him to be deported to India, PPBM strategist Rais Hussin said.
External Affairs Ministry Spokesperson Raveesh Kumar said India has friendly ties with both the countries.
Online reports said there were at least 40,000 protesters in the rally in downtown Kuala Lumpur.
'None of these three countries -- Turkey, Iran or Malaysia -- ever made a hostile move against India to support the Pakistan-based terrorist elements,' notes Ambassador M K Bhadrakumar.
'Who put the fear of god into Imran Khan and how it happened we do not know, but the great cricketer panicked and called Mahathir to regret that he cannot attend the KL Summit,' notes Ambassador M K Bhadrakumar.
The opposition parties vehemently criticised the new 'one nation, one tax' system having four different rates instead of a single rate adopted in some countries including the UK and Singapore.
Moon Jae-in's visit will play a crucial role in exploring complementarities between India's Act East policy and South Korea's New Southern policy, says Dr Rahul Mishra.
'Clearly, the warming of ties can be a 'win-win' for India and China,' says Ambassador M K Bhadrakumar.
Prime Minister Narendra Modi had invited ASEAN leaders to be the chief guests.
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