Obama will become the first sitting US president to visit Malaysia in nearly half a century when he touches down in the country on April 26.
Washington has expressed disquiet about what it says are politically motivated charges to keep the veteran opposition leader out of Malaysian politics.
In March, the Malaysian Court of Appeals overturned Anwar's 2012 acquittal on sodomy charges which date from a bitter power struggle with his then rival, prime minister Mahathir Mohamad, in the 1990s.
Anwar, 66, was sentenced to five years in jail but is currently free pending an appeal to the Federal Court, Malaysia's highest judicial body.
Asked whether Obama would make time during his schedule in Malaysia, which includes a state dinner and talks with Prime Minister Najib Razak, national security advisor Susan Rice indicated he would not.
"I think that the president is not likely to have that meeting -- there may be other engagements at other levels," said Rice.
Obama will however hold a town hall meeting with what he calls young leaders from all over Southeast Asia and will also meet civil society representatives in Kuala Lumpur.
Obama's trip, which begins in Japan, also includes stops in South Korea and the Philippines.