Anwar also pledged to continue working with Myanmar, including on the repatriation of thousands of Myanmar nationals from Malaysia - a move that has been widely criticised by the United Nations and rights groups concerned about the risks from an ongoing civil war.
Former Myanmar junta chief Min Aung Hlaing is on a two-day visit to Malaysia as he seeks greater international legitimacy after becoming president in April following an election that Western nations and rights groups widely criticised as a sham.
Myanmar has been in turmoil since 2021 when Min Aung Hlaing led a military coup against a democratically elected government, triggering armed conflict across much of the country.
Min Aung Hlaing and other senior Myanmar officials have been barred from attending summits of the Association of Southeast Asian Nations (ASEAN) after failing to adhere to an ASEAN-brokered peace plan following the coup, but some member countries have sought to re-establish ties.
Since becoming president, Min Aung Hlaing has also visited ASEAN members Thailand, Laos, Cambodia and Vietnam.
Anwar acknowledged ongoing concerns about democratic processes in Myanmar but said differences must be respected, adding that Min Aung Hlaing had shown a willingness to be collaborative.
"I would say that we and our part in Malaysia, will do whatever is possible to make sure that we enhance this collaboration and ultimately, take Myanmar as part of our community of nations, without prejudice, and particularly in the context of ASEAN," Anwar told a media briefing following the meeting on Thursday.
Anwar also expressed appreciation to Min Aung Hlaing for accepting the repatriation of more than 10,000 Myanmar nationals from Malaysia.
Malaysia has said it can no longer take in refugees from Myanmar, saying they had become a financial burden and a security risk.
Malaysia is not a party to the UN refugee convention and treats asylum-seekers as illegal migrants.
The country in September sent back about 1500 people on Myanmar naval ships, part of a wider repatriation program that could see as many as 5000 people deported.
Min Aung Hlaing said at Thursday's briefing Myanmar citizens held at Malaysian immigration detention centres would be brought back as soon as possible.
He also extended an invitation for Anwar to visit Myanmar "when the time is right".
Anwar and Min Aung Hlaing did not mention if their discussions included plans to repatriate Rohingya Muslim refugees, many of whom fled Myanmar after a brutal 2017 military crackdown in the country's Rakhine state that is now the subject of a genocide case at the International Court of Justice.
