President George W Bush has urged US legislators not to pass a resolution declaring the killing of Armenians by Ottoman Turks to be genocide.
Turkish Prime Minister Recep Tayyip Erdogan said the bill's passing would result in a "significant weakening" of his country's ties with the US.
The country is a regional operational hub for the US military, which uses its airspace to supply US forces in Iraq.
Turkey admits many Armenians died in World War I but denies genocide.
"This resolution is not the right response to these historic mass killings," Mr Bush said just before the House Foreign Affairs Committee began debating the resolution.
Such a move, already taken by France's parliament for one, would do "great harm" to US relations with Turkey, Mr Bush added.
It is highly unusual for the White House to make such a dramatic last-minute intervention in Congressional business, the BBC's Justin Webb reports from Washington.
With the opposition Democrats now in charge in Congress, they could force a vote, dealing a potentially grave blow to the Bush administration's efforts to keep Turkey on side, our correspondent adds.
Even if the bill passes and is then adopted by the House, it will not be binding.
Turkey has seen angry rallies demanding action in Iraq
But the BBC's Sarah Rainsford, in Istanbul, says that this will have little impact on the reaction in Turkey which had pulled out all the stops to prevent the genocide resolution reaching Congress.
Tom Lantos, chairman of the Foreign Affairs Committee, admitted the resolution posed a "sobering" choice as the debate opened.
"We have to weigh the desire to express our solidarity with the Armenian people... against the risk that it could cause young men and women in the uniform of the United States armed services to pay an even heavier price than they are currently paying," he said.
Mr Lantos, himself a survivor of the Jewish Holocaust, said he would introduce a resolution praising US-Turkish friendship next week, according to AFP news agency.
US Defense Secretary Robert Gates earlier said that 70% of US air cargo for Iraq went through Turkey, as well as about a third of the fuel used by the US military there.
"Access to airfields and to the roads and so on in Turkey would very much be put at risk if this resolution passes and Turkey reacts as strongly as we believe they will," he added.
The debate comes amid mounting anger in Turkey that the US is not doing enough to counter the Kurdish separatist PKK group, which mounts deadly attacks on Turkey from inside Iraq, our correspondent in Turkey says.
Mr Erdogan said the government was preparing a motion seeking approval to launch military action in Iraq, which might go before parliament as soon as Thursday.
The White House has warned Turkey not to send in troops
Armenia alleges that up to 1.5 million Armenians were killed in an organised campaign to force them out of what is now eastern Turkey in 1915-17.
That is strongly denied by Turkey, which says that large numbers of both Turks and Armenians were killed in the chaos surrounding World War I and the collapse of the Ottoman Empire when Armenians rose up.
Last year, the lower house of the French parliament declared the killings of Armenians a genocide.