U.S. President Barack Obama will "very directly" raise concerns about the status of the opposition and respect for human rights when he visits Malaysia, Deputy National Security Adviser Ben Rhodes said on Thursday.

Rhodes, speaking to reporters at an Asia-Pacific summit in Manila, said Obama would have a bilateral meeting with Malaysian Prime Minister Najib Razak in Kuala Lumpur on Friday, ahead of the weekend East Asia summit.

The visit is Obama's second to Malaysia in two years. In December 2014, Obama played golf with Najib in Hawaii, which some commentators said illustrated the close personal relations between the two leaders.

"We are going to be very candid about areas where we have disagreements and differences and frankly objections, if we see that the type of universal values that we support are not being respected," Rhodes said.

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Tens of thousands of Malaysians rallied to call for Najib's resignation in August on corruption issues. A report in July said investigators looking into alleged financial wrongdoing at debt-ridden state fund 1Malaysia Development Berhad (1MDB) had traced a payment of nearly $700 million going into Najib's personal bank accounts.

Najib is the chairman of the advisory board of the fund, which has debts of more than $11 billion. Reuters has not verified the report.

Najib has denied any wrongdoing. Malaysia's anti-graft agency said the money was a "donation" from the Middle East.

Malaysian authorities have cracked down on organisers of anti-government rallies critical of Najib and 1MDB, blocked websites, and suspended newspapers reporting extensively on 1MDB's woes, prompting a watchdog to say human rights have deteriorated under Najib's watch.

"The president ... will raise with Prime Minister Najib concerns we have about the status of the political opposition in Malaysia, the imprisonment of elements of that opposition or of free media and civil society that are such important components of democracy," Rhodes said. "He will raise those issues very directly."

Rhodes said Obama will also meet representatives of Malaysia's civil society and youth organisations.