Experts estimate rich nations will need to donate at least $10 billion a year if the AIDS epidemic is to be brought under control. That compares to overall spending this year of about $2.8 billion.
About 40 demonstrators chanting "Shame! Shame!" and waving placards reading "Wanted: Bush and Thompson for murder and neglect of people with AIDS," marched down the center aisle of the lecture hall and lined up on stage as Thompson spoke.
Security guards formed a barrier between Thompson and the protesters. Thompson went on to deliver his speech, but his words were drowned out by whistle blowing and protests shouted through a bullhorn.
"The United States is passionately committed to this international fight," he said, speaking to reporters after he had finished his speech.
"I understand that people are passionate about this and want to blame the United States," Thompson said. "But the United States under President Bush has doubled the amount of resources it provides for the fight against AIDS."
Last month, President Bush announced a five-year, $500 million initiative to stem transmission of HIV from mother to child in Africa and the Caribbean. More than 2 million women carrying the AIDS virus give birth each year, and 90 percent pass it on to their babies during pregnancy, childbirth or nursing.
Critics called the proposal "grossly underfinanced."
AIDS activists want the United States to contribute more to the United Nations-backed Global Fund to Fight AIDS, Tuberculosis and Malaria. The United States has pledged $500 million to that fund.
"I understand that people want to yell and scream," Thompson said, "but they would serve their cause much better ... if they would help other countries see the light and encourage them to contribute like the United States has."
Thompson said 45 percent of money committed to HIV programs worldwide comes from the United States and the American contribution to the Global Fund represents 25 percent of the total money given so far.
However, Jeffrey Sachs, an economist from Columbia University who chaired a World Health Organization committee on how much money is needed to fight AIDS, said the United States has not contributed its fair share and should be donating $2.5 billion a year.
"Secretary Thompson was probably surprised at his reception today. He should not be surprised. It is a reflection of the utter confusion within the United States government of what they are actually doing," Sachs said.
"They believe they are doing the right thing," he said. "They pick numbers out of the air week to week. They have not budgeted systematically over the next few years and when I inquired about this at the White House ... the responses I have got show that they have not done their homework."
The weeklong meeting in Barcelona, attended by 15,000 delegates, has thrown into sharp relief the difference in prospects for those in Western countries and those in the developing world who are infected with the virus that causes AIDS. Those in the poorer group account for 95 percent of infections.
A stream of new antiretroviral drugs in recent years mean AIDS is no longer an automatic death sentence. But it continues to claim millions of lives in poor countries where expensive combination therapy is available to only a few.