The Obama administration is facing internal dissent from its scientists for approving the use of huge quantities of chemical dispersants to tackle the oil spill in the Gulf of Mexico, the Guardian has learned.

The US Environmental Protection Agency has come under attack in Congress and from independent scientists for allowing BP to spray almost 2m gallons of the dispersant Corexit on to the slick and, even more controversially, into the leak site 5,000ft below the sea. Now it emerges that EPA's own experts have been raising similar concerns within the agency.

Jeff Ruch, the exective director of the whistleblower support group Public Employees for Environmental Responsibility, said he had heard from five scientists and two other officials who had expressed concerns to their superiors about the use of dispersants.

"There was one toxicologist who was very concerned about the underwater application particularly," he said. "The concern was the agency appeared to be flying blind and not consulting its own specialists and even the literature that was available."

Veterans of the Exxon Valdez spill questioned the wisdom of trying to break up the oil in the deep water at the same time as trying to skim it on the surface. Other EPA experts raised alarm about the effect of dispersants on seafood.

Ruch said EPA experts were being excluded from decision-making on the spill. "Other than a few people in the united command, there is no involvement from the rest of the agency," he said. EPA scientists would not go public for fear of retaliation, he added.

Jerrold Nadler, a New York Democrat who introduced a ban on dispersants pending further testing in an oil spill bill passed by the House of Representatives last week, said the EPA had failed in its duty to protect the environment.

"We are undertaking a huge uncontrolled experiment with the entire Gulf," he said. "They have fallen down on the job very substantially because they allowed BP to use dispersants. Even when they told BP not to use dispersants they allowed BP to ignore their advice."

Independent scientists also criticised the EPA for claiming that the combination of oil and dispersants posed no greater danger to marine life on its own.

On Wednesday, a toxicologist from Texas Tech University is scheduled to tell a Senate hearing that the unprecedented use of dispersants "created an eco-toxicological experiment".

"The bottom line is that a lot of oil is still at sea dispersed in the water column," said Ron Kendall. "It's a big ecological question as to how this will ultimately unfold." Previous studies, including a 400-page study by the National Academy of Sciences, have warned that the combination of oil and dispersants is more toxic than oil on its own, because the chemicals break down cell walls, making organisms more susceptible to oil.

The EPA issued a report on Monday, based on a study of how much of the mixture was needed to kill a species of shrimp and small fish, just two of the 15,000 types of marine life in the Gulf. The EPA test did not address medium- or long-term effects, or reports last week that dispersants were discovered in the larvae of blue crab, entering the food chain.

"It was only one test and it was very crude. We knew going into this and the EPA knew that this mixture is highly toxic to many, many species. There is a whole weight of literature," said Susan Shaw, the director of the Marine Environmental Research Institute, who has been organising on the issue. "It is not the whole science. It's the convenient science."

Hugh Kaufman, a senior EPA policy analyst, dismissed the tests as little more than a PR stunt. "They are trying to spin this limited piece of information to make it look like dispersants are safe and that the Corexit dispersant is safe."

EPA did not immediately respond to requests for comment. It is under fire from Congress for allowing BP and the coast guard to ignore its order last May to cut the use of dispersants by 75%. Documents released by the Massachusetts Democrat Ed Markey this week show the EPA allowed spraying of dispersants 74 times over a period of 48 days. At times, the EPA gave advance approval for the use of dispersants for up to a week. The documents also showed the EPA allowed BP to spray 36,000 gallons of Corexit in a single day. The controversy surrounding EPA's role in the oil spill marks a turning point for the Obama administration, which came to power vowing to repair the frayed relationship between scientists and government under George Bush and promising a new era of transparency.

Nine leading scientists have written a public letter calling on BP and the Obama administration to release all scientific data related to the spill, including wildlife death. "Just as the unprecedented use of dispersants has served to sweep millions of gallons of oil under the rug, we're concerned the public may not get to see critical scientific data until BP has long since declared its responsibility over," said Bruce Stein of the National Wildlife Federation.