The French minister in charge of humanitarian relief called on the UN to "clarify" the American role amid claims the military build up was hampering aid efforts.
Alain Joyandet admitted he had been involved in a scuffle with a US commander in the airport's control tower over the flight plan for a French evacuation flight.
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"This is about helping Haiti, not about occupying Haiti," Mr Joyandet said.
Geneva-based charity Medecins Sans Frontieres backed his calls saying hundreds of lives were being put at risk as planes carrying vital medical supplies were being turned away by American air traffic controllers.
But US commanders insisted their forces' focus was on humanitarian work and last night agreed to prioritise aid arrivals to the airport over military flights, after the intervention of the UN.
The diplomatic row came amid heightened frustrations that hundreds of tons of aid was still not getting through. Charities reported violence was also worsening as desperate Haitians took matters into their own hands.
The death toll is now estimated at up to 200,000 lives. Around three million Haitians – a third of the country's population – have been affected by Tuesday's earthquake and two million require food assistance.
While food and water was gradually arriving at the makeshift camps which have sprung up around the city, riots have broken out in other areas where supplies have still not materialised.
Haiti was occupied by the US between 1915 and 1935, and historical sensitivities together with friction with other countries over the relief effort has made the Americans cautious about their role in the operation.
American military commanders have repeatedly stressed that they are not entering the country as an occupying force.
US soldiers in Port-au-Prince said they had been told to be discreet about how they carry their M4 assault rifles.
A paratrooper sergeant said they were authorised to use "deadly force" if they see anyone's life in danger but only as a "last resort".
Capt John Kirby, a spokesman for the joint task force at the airport, said the US recognised it was only one of a number of countries contributing to a UN-led mission.
He also emphasised the US troops, which he said would rise to 10,000 by Wednesday would principally be assisting in humanitarian relief and the evacuation of people needing medical attention.
The main responsibility for security rests with the UN, which is to add a further 3,000 troops to its force of 9,000.
However, it was agreed on Sunday night that the Americans would take over security at the four main food and water distribution points being set up in the city, Capt Kirby said.
"Security here is in a fluid situation," he said. "If the Haitian government asked us to provide security downtown, we would do that." He played down the threat of violence, saying: "What we're seeing is that there are isolated incidents of violence and some pockets where it's been more restive, but overall it's calm."