Human rights groups have been urging Mr. Obama to meet with opposition leader Anwar Ibrahim while the president is in the country as part of his four-nation Asia tour. Instead, Mr. Obama is sending national security adviser Susan Rice to meet Anwar on Monday.
Mr. Obama cited freedom of the press, human rights and civil liberties as issues that he said are always on the agenda when he travels the world. He downplayed the fact that a meeting with Anwar wasn't on his schedule.
"The fact that I haven't met Mr. Anwar in and of itself is not indicative of our lack of concern, given the fact that there are a lot of people I don't meet with and opposition leaders that I don't meet with," he said at a joint news conference with Prime Minister Najib Razak after the two met privately. "That doesn't mean I'm not concerned about them."
Mr. Obama, who met with Najib during a historic, two-day visit to Malaysia, defended the government's handling of the search for missing Malaysia Airlines Flight 370. He also said Russia will soon be hit with new sanctions because Russian President Vladimir Putin's government has "not lifted a finger" to help diffuse tensions in Ukraine.
Anwar, a former deputy prime minister, was recently convicted for the second time on sodomy charges that the U.S. and international human rights groups have challenged as politically motivated. He presents the most potent political threat to Najib, whose popularity has declined over the past two elections.
Mr. Obama said Najib has made progress on human rights in his country and would be the first to acknowledge having more work to do to improve the climate. Mr. Obama said he shared with Najib his own view that countries will be better off in the long run if they respect the rule of law and basic freedoms - "even when it drives you crazy, even when it's inconvenient."
The United States still has work to do on these issues, too, the president added.
On tensions between Russia and Ukraine, Mr. Obama said there's strong evidence Russia is encouraging destabilizing activities in eastern and southern Ukraine. He blamed Russia for failing to uphold terms of a recent deal reached in Geneva with Russia, the U.S., the European Union and Ukraine.
The accord calls on Russia to pull back its forces from the border with Ukraine and encourage pro-Russian separatists to turn over buildings they're occupying in eastern Ukraine. Speaking a day before the U.S. was expected to levy new sanctions against Russia, Mr. Obama said what the accord "asks of Russia is hardly onerous."
At the same time, he resisted suggestions that the U.S. should levy unilateral sanctions against Russia's economy, arguing the ability to deter Putin will be enhanced once Putin sees the world is unified in sanctioning Russia. The U.S. and Europe must act collectively, Mr. Obama said.
Mr. Obama said Russia wants to portray the Ukraine crisis through a Cold War prism that pits Washington against Moscow. He says that's not the issue: it is Ukraine's independence and sovereignty.
He also said there's strong evidence Russia is encouraging destabilizing activities in eastern and southern Ukraine.
Obama departs Malaysia on Monday for the Philippines, following earlier stops in Japan and South Korea.
The United States and the Philippines have reached a 10-year agreement that would allow a larger U.S. military presence in this Southeast Asian nation as it grapples with increasingly tense territorial disputes with China, White House officials said Sunday.
Two Philippine officials confirmed the agreement to The Associated Press before the White House announcement.
The Enhanced Defense Cooperation Agreement would give American forces temporary access to selected military camps and allow them to preposition fighter jets and ships. It will be signed Monday at the main military camp in the Philippine capital, Manila, before President Barack Obama arrives on the last leg of a four-country Asian tour, following earlier stops in Japan, South Korea and Malaysia.
A Philippine government primer on the defense accord that was seen by the AP did not indicate how many additional U.S. troops would be deployed "on temporary and rotational basis," but it said that the number would depend on the scale of joint military activities to be held in Philippine camps.
The size and duration of that presence still has to be worked out with the Philippine government, said Evan Medeiros, senior director for Asian affairs at the White House's National Security Council.
Medeiros declined to say which specific areas in the Philippines are being considered under the agreement, but said the long-shuttered U.S. facility at Subic Bay could be one of the locations.
The two Philippine officials spoke with the AP on condition of anonymity because they were not authorized to discuss details of the pact before it is signed.
The defense accord is a new milestone in the longtime treaty allies' relationship and would help address their respective dilemmas. With its anemic military, the Philippines has struggled to bolster its territorial defense amid China's increasingly assertive behavior in the disputed South China Sea. Manila's effort has dovetailed with Washington's intention to pivot away from years of heavy military engagement in the Middle East to Asia, partly as a counterweight to China's rising clout.
"The Philippines' immediate and urgent motivation is to strengthen itself and look for a security shield with its pitiful military," Manila-based political analyst Ramon Casiple said. "The U.S. is looking for a re-entry to Asia, where its superpower status has been put in doubt."