The National Aeronautics and Space Administration (NASA) had planned to use the U-Tapao air base, 190 kilometres (120 miles) southeast of Bangkok, for its study of monsoon weather patterns in August and September.
But Thailand's government missed a deadline to approve the scheme leaving NASA short of the necessary "lead time" to transport equipment, hire staff and build laboratories for the study, an embassy spokesman in Bangkok said.
"It is unfortunate to lose this important opportunity for NASA and Thai scientists to collaborate to collect data of scientific importance to not only our two countries but others in the region as well," said spokesman Walter Braunohler.
"It is too early to say at this time whether resources will be available to revisit the project next year."
The issue is the latest in a series of bitter rows between the Pheu Thai ruling party of Prime Minister Yingluck Shinawatra -- the sister of ousted premier Thaksin -- and the main opposition Democrat Party, who respectively represent the nation's "Red" and "Yellow" shirt factions.
Yingluck had endorsed the project, but retreated from approving it amid fierce criticism from the opposition, which claimed a deal had been struck allowing the NASA study in exchange for granting a US visa to Thaksin -- who lives in self-imposed exile.
The Democrats also raised fears the study could compromise Thai sovereignty and impact on the country's relations with China, which is carefully watching US moves to establish further footholds in Southeast Asia.
Democrat leader Abhisit Vejjajiva, who was succeeded as prime minister by Yingluck in 2010, said the government had failed to sell the benefits of the project.
"It's the government's responsibility to use the half year they had but they did not explain the project to the public," he told AFP.
"During this time the government should have talked with friendly neighbours to make them comfortable (with the project)," he said, without saying which nations he was referring to.
A senior Science Ministry official said it was "pity" for flood-prone Thailand to miss the chance to "fully understand global climate" on account of a political wrangle.
"Thailand may appear a bit strange in the eyes of international scientific community because this is pure science, but we have unnecessarily tied the issue to politics," Anond Snidvongs, director Geo-Informatics and Space Technology Development Agency said.
The US has a long association with U-Tapao, using it as an airbase for its B-52 bombers during the Vietnam War.