President Reagan today reaffirmed his commitment to "free markets and free trade" as he stopped here en route to Indonesia on a Pacific Basin trip that has been dogged in early stages by controversies over human rights and press freedom.

The president said he will be bearing a "message of freedom" when he arrives in Indonesia tonight for a meeting of the Association of Southeast Asian Nations (ASEAN), which includes Indonesia, the Philippines, Malaysia, Thailand, Singapore and Brunei.

"And we will reassert our belief that, in liberty, we can work together to bring still greater prosperity to the Pacific," Reagan said to a crowd of about 2,500 people.

But White House spokesman Larry Speakes said earlier in Honolulu, where the president rested over the weekend, that Reagan will not make an issue of restraints on civil liberties in Indonesia, where a widespread crackdown on dissidents has been reported before the ASEAN meeting. Speakes said, "The president has strong feelings on human rights, but it is a matter that he believes is most effectively handled through private exchanges."

A group of 125 House members sent Reagan a letter, released Monday, asking that he raise concerns during his visit to Indonesia about alleged human rights violations on the Indonesian-held island of East Timor. A group of 23 senators made a similar request.

The groups cited reports of armed conflict, disappearances, executions, torture and compulsory birth control on the Pacific island, which was invaded by Indonesia in 1975.

However, Reagan does plan to make a major point at the ASEAN meeting on human rights violations committed by the communist government of Vietnam, White House officials said Monday. The president reportedly will reaffirm that the United States will not recognize Vietnam as long as it occupies Cambodia, even if the Vietnamese decide to cooperate more fully and provide information on missing U.S. servicemen.

Speakes said Sunday that "the most systematic, widespread violations of human rights in Southeast Asia are those in Vietnam and now in Vietnam-occupied Cambodia."

Senior U.S. officials acknowledge they have been embarrassed by the refusal of the Indonesian government to heed U.S. pleas and admit Australian journalists traveling on the media plane accompanying Reagan to Indonesia.

The status of the two correspondents of the Australian Broadcasting Co. was unclear today. They had continued on the trip to here after the Australian foreign ministry asked Indonesia to admit them to Bali, where the ASEAN meeting will be held. On Sunday, the Australians had announced they were dropping off the White House news charter and flying to Tokyo for the Economic Summit.

Indonesia had barred the Australians from covering the ASEAN meeting in retaliation for an April 10 article in the Sydney Daily Mail alleging that Indonesian President Suharto had enriched himself and business associates through government favoritism.

Reagan also was enmeshed in controversy in Honolulu because he insisted on telephoning deposed Philippine president Ferdinand Marcos on the ground that Marcos had been a longtime friend and ally of the United States. In an effort to head off resentment in the Philippines over this action, Speakes has repeatedly reaffirmed Reagan's support of the government of President Corazon Aquino.

Reagan is to meet with Philippine Vice President Salvador Laurel in Bali on Thursday and express U.S. support of the Aquino government's reforms. However, White House officials said Reagan will not change his schedule to stop in the Philippines on his return from the Economic Summit, as Laurel has suggested.

In his remarks here, where he was scheduled to stay less than two hours during a refueling stop early this morning, Reagan repeated the major theme of his trip: that there is a "necessary connection" between freedom and economic growth.

"The foreign ministers I will meet with in Indonesia represent nations that have each in large part embraced human liberty, both political and economic, and in recent years the people of these nations have produced a remarkable record of economic growth," Reagan said.

He also said that Guam, 9,000 miles from Washington, "shines forth as a beacon of democracy" and he paid tribute to the large number of Guamanians serving in the U.S. armed forces.