The US Aids co-ordinator was heckled by about 50 activists as he addressed a global Aids summit in Thailand.
Dozens of opponents sat in front of the speaker's podium
Protestors chanted "Bush lies, millions die" before Randall Tobias launched his defence of US policy on combating Aids.
Critics have attacked US trade deals with poorer nations, and say strings are attached to US anti-Aids funding.
Mr Tobias called for unity in fighting the disease and said the US was spending twice as much as other donor nations combined.
Far fewer US government-employed scientists are attending the conference than in previous years. Washington says this is because of financial considerations.
But some scientists have said it was because Tommy Thompson, US Secretary of Health and Human Services, was not well received at the last conference two years ago.
"At this time, perhaps the most critical mistake we can make is to allow this pandemic to divide us," Mr Tobias told the conference, as protesters sat in front of the podium.
"We are striving toward the same goal - a world free of
HIV/Aids. When 8,000 lives are lost to Aids every day,
division is a luxury we cannot afford.
"It is morally imperative that we direct our energies at these enemies, not at one another."
On Tuesday - in a veiled attack on the US - France criticised bilateral trade deals that force poor nations to give up rights to make cheaper anti-Aids drugs.
But US officials said their trade deals were in line with World Trade Organisation rules.
Earlier, UN Secretary General Kofi Annan urged Washington to show the same commitment to the fight against HIV/Aids as to the war on terror.
Washington has earmarked $15bn over five years to tackle the disease, according to the UNAids agency.
But the US has come under fire for its policy of ensuring much of the money is channelled bilaterally, rather than through the multilateral global Aids fund.
The Bush administration also advocates sexual abstinence as the best way to stop the disease spreading.
The administration has a stipulation that 30% of US anti-Aids funds go through faith-based organisations, which typically support the abstinence policy.
Many scientists and activists, however, favour encouraging the use of condoms.
Mr Tobias praised Ugandan President Yoweri Museveni who has backed the abstinence approach.
"We must learn from his leadership in the fight against Aids. Abstinence works... being faithful works... condoms work. Each has its place," he said.