The 71-year-old airline has been on the ropes since 2014 when Flight MH370 disappeared and MH17 was shot down by a Russian-made missile over war-torn Ukraine.
Mahathir, 93, is in the Philippines for the first time since his shock election victory last year.
The Ministry of External Affairs (MEA) had in January 2016 made a formal request to Malaysia to deport Naik.
He said the government wants to create legal channels for overseas Pakistanis to send their remittances through.
Mahathir pointed out that 65 per cent of the regional bloc's trade was with the 16 members of the proposed Regional Comprehensive Economic Partnership, asking nations to participate in it.
Malaysia's leader courted Chinese e-commerce investment in his country today, the start of his first trip to China since his stunning electoral victory three months ago.
India had made a formal extradition request for Naik, who left the country in 2016, to be returned to the country after accusing him of inciting youngsters to commit terror activities through his hate
Mahathir last week said the cleric would not be handed over to Indian authorities as he had been granted Malaysian permanent resident status.
Mahathir said that the government would not deport Naik as he has been granted Malaysian permanent resident status, unless he causes trouble in the country.
After delivering a talk in New Delhi on "Indo-Bangladesh: Historical and contemporary perspective", Hossain Toufique Imam, political advisor to Hasina, answered a question from a reporter on Naik.
Zakir Naik, a radical television preacher, reportedly left India in 2016 and subsequently moved to largely Muslim Malaysia, where he was granted permanent residency.
The pardon allows Anwar to re-enter active politics immediately, but it was not clear what his role in government would be.
Mahathir, 92, was yesterday sworn in as the seventh prime minister of Malaysia.