The White House was accused today of spinning a government scientific report into the amount of oil left in the Gulf of Mexico from the BP spill which had officials declaring that the vast majority of the oil had been removed.

As BP workers finished pouring cement into the well as a first step to permanently sealing it today, environmental groups and scientists – including those working with government agencies to calculate the scale and effects of the spill – said White House officials had painted far too optimistic a picture of a report by the National Oceanic and Atmospheric Agency (Noaa) into the fate of the oil.

"Recent reports seem to say that about 75% of the oil is taken care of and that is just not true," said John Kessler, of Texas A&M University, who led a National Science Foundation on-site study of the spill. "The fact is that 50% to 75% of the material that came out of the well is still in the water. It's just in a dissolved or dispersed form."

With work progressing on the final phase of the "static kill" sealing of the well, Thad Allen, the Obama administration's top official on the spill, told reporters there would be no new oil in the Gulf.

But those assurances failed to satisfy scientists and environmental groups, who disputed the claim by Carol Browner, the White House energy and climate adviser, that "the vast majority of oil is gone".

In Louisiana, state wildlife officials told CNN that tar balls and patches of oil were still washing up in the marshes and coastal areas of St Bernard, Plaquemines and Jefferson parishes.

Susan Shaw, a marine toxicologist and director of the Marine Environmental Research Institute, said the White House had been too quick to declare the oil was gone. "The blanket statement that the public understood is that most of the oil has disappeared. That is not true. About 50% of it is still in the water," she said.

Like other scientists, she said the report failed to explain how it reached its estimates on the amount of oil that was biodegraded naturally, or dispersed with chemicals. "There are a lot of unanswered questions."

Even the White House's own estimates still left a spill five times the size of that from the Exxon Valdez, she said, with long-term consequences that would be unknown for years to come.

Terry Hazen, the head of ecology at the Lawrence Berkeley national laboratory, who studied the spill for Noaa, said his teams could find no trace of oil on the surface or in the deep between 2km and 100km from the well site last week.

"Whatever was put into the environment, it is undetectable in the water column and the surface of water," he said. But he added: "That is not true though in the marshes or on some of the shorelines. We do know there is still oil out there."

He also said there were potential weaknesses in the analysis because of Noaa's assumptions about the size of the spill.

"When they do all of the inventories trying to estimate all of the oil and where it went there is pretty wide margins of estimates of how much was actually coming out of the well head," he said. "That complicates everything."

However, such nuances were overshadowed by the White House, which staged a high-profile event on Wednesday to announce that the well had stopped flowing, and that the consequences of the spill were not as catastrophic as once feared.

Francesca Griffo, senior scientist at the Union of Concerned Scientists, said the White House had stepped on more nuanced statements from Noaa scientists. "When these reports go through the spin machine they get distorted," she said. "If you look closely at this report, it makes it very clear that this is not over."

Rick Steiner, a former University of Alaska marine biologist, suggested that the White House had been too eager to try to put the oil spill behind it, with Democrats in Congress facing tough election fights in November.

"It seems that there was a rush to declare this done, and there were obvious political objectives there," he said. "Even if there is not a drop of oil out there, and it had truly magically vanished, it would still be an environmental disaster caused by the toxic shock of the release of 5m barrels of oil."