"She has expressed this before in Asean (the Association of South East Asian Nations) and the fact that she took this up directly is a signal of our hope that democratic reforms will take place as soon as possible," Bunye told reporters.
Suu Kyi has spent more than half the time since 1989 under house arrest. Her latest spell began in May 2003.
The military, which has ruled in one guise or another since 1962, refused to acknowledge her party's landslide election victory in 1990 and has detained hundreds of opposition figures.
About 40 human rights activists held a rally outside the presidential palace in Manila to protest against the brief visit by Soe Win, who arrived on Sunday evening and flew home on Monday afternoon.
Soe Win took over as prime minister in October after his predecessor, Khin Nyunt, was ousted after a lengthy power struggle with rival generals. Khin Nyunt was regarded by diplomats as one of Myanmar's more pragmatic generals.
The Philippines, which returned to democracy after the 1986 ouster of dictator Ferdinand Marcos, and Myanmar are among the 10 members of Asean.
Members usually avoid criticism of each other's internal affairs although the Philippines has in the past spoken out against Myanmar's poor rights record and its suppression of democracy.
Arroyo made no mention of human rights in a speech during an official luncheon for Soe Win but congratulated him for visiting his Asean neighbours.
Soe Win said in his speech Myanmar was on its way to becoming a "modern, disciplined democratic nation" with the start last week of a convention meant to set the course for a new constitution and the return of multi-party democracy.
"Once its task is completed, a new constitution will emerge and the aspirations of our people will be met," he said.
Human rights groups and many Western governments have criticised the process as a sham because the military has already set out the agenda, most delegates are hand-picked and the opposition is not taking part.