"Apparently, some states were unwilling to accept the entry of Haitian patients for follow-on critical care," US Transportation Command spokesman Captain Kevin Aandahl told AFP.
"Without a destination to fly to, we can't move anybody."
The US State Department and Defense Department were working with Florida authorities to try to fix the problem, said US Ambassador to Haiti Kenneth Merten, but aid groups warned it could be too late.
"People are dying in Haiti because they can’t get out," Barth Green of Project Medishare for Haiti, a nonprofit group which has been evacuating about two dozen patients a day, told The New York Times.
The United States has spearheaded relief efforts since the 7.0-magnitude quake, which killed around 170,000 people, injured around 200,000 and leveled much of the capital Port-au-Prince.
Washington has deployed around 20,000 troops and a hospital ship to the stricken Caribbean nation. US officials said Saturday that American civilian and military staff had treated 37,500 injured Haitians.
The aid effort as a whole has, however, drawn criticism for a lack of coordination. Several leftist Latin American nations have accused US forces of occupying Haiti militarily instead of focusing on aid needs.
Ecuadoran President Rafael Correa, who left Haiti on Saturday after a two day visit, highlighted what he called the "imperialism" of aid efforts.
"They donate first, but most of it goes back to them," he said at a joint press conference with Haiti's President Rene Preval, criticizing both military aid efforts and those of foreign NGOs.
Quake-hit Haitians, many of whom are living in squalid makeshift tent camps, have complained that the huge influx of food, water and shelter since the disaster has been slow to reach them on the ground.
The UN World Food Program said it would open 16 fixed collection sites across the capital on Sunday in a bid to reduce long and often chaotic food lines at mobile handouts.
Only women will be allowed to enter the sites to pick up supplies using coupons. Many of handouts have turned into dangerous scrums where women and children are shoved aside.
"Until now we've been in what we would call a quick and dirty phase, but this more robust distribution system will allow us to reach more people more quickly," said WFP spokesman Marcus Prior.
Tent camps outside the capital that the government said would ease the pressure on Port-au-Prince have finally begun to open, but for some the squalid conditions are too much.
A rickety boat carrying 126 Haitian migrants was picked up earlier this week off the Turks and Caicos Islands, the first group known to have fled since the earthquake, police said. The islands are a frequent stopover point for Haitians seeking to land in the US state of Florida.
"The amount of people on board is indicative of the problem we may now face," the British dependency's marine police chief Neil Hall said.
Diseases such as diarrhea, measles, and tetanus were rising in the tent settlements, prompting UN agencies and Haiti's government to prepare a mass vaccination drive.
Survivors also face rising insecurity with reports of rape and violence plaguing the weak and vulnerable.
And in a further blow to efforts to rebuild, Port-au-Prince's iconic Iron Market, built in 1889, was ravaged by fire on Friday and left to burn for hours by overstretched firefighters.
Aid officials have warned that the reconstruction process in Haiti, already the poorest country in the western hemisphere, will take decades.
But the UN says aid donations and pledges have passed two billion dollars, and former US President Bill Clinton urged business chiefs at the World Economic Forum in Davos this week to invest in Haiti's future.