Reuben Baris, the acting chief of the herbicides branch of the E.P.A., said that 2,708 complaints had been reported to state agriculture officials about dicamba crop damage as of mid-October. They came from 25 of the 34 states where the “over the top” application is approved for use. The largest number of complaints were filed in Arkansas, where there were 986 incidents, and Missouri, which had 310.

Mr. Baris suggested the number of complaints understated the problem because most incidents went unreported. He estimated the actual number of damage incidents could be five times greater than the Missouri researchers found.

“It is an extremely high profile and significant situation,” Mr. Baris said, calling the crop damage that has occurred “unacceptable.”

The agency is still awaiting data on how the problem has affected soybean crop yields.

The E.P.A., when it approved the “over the top” use of dicamba, notified the three manufactures that they would have to secure new approval of its use after two years. And Mr. Baris and Mr. Keigwin made clear on Wednesday that approval might be in jeopardy if the measures being taken for the next growing season did not significantly reduce the scope of the drift damage.

Sale of genetically modified seeds and related herbicides is worth tens of millions of dollars to these companies, which have already faced challenges as weeds have been growing resistant to another popular herbicide they sell, glyphosate.

An estimated 22 million acres of soybean crops were planted with dicamba-tolerant G.M.O. seeds and treated with the “over the top” approach this year, out of the total estimated 89.5 million acres of soybeans planted nationwide.

Some pesticide industry officials question whether the 3.6 million acre estimate represents the total number of acres for any farm that has even a small amount of damage, meaning actual crop damage might be much smaller.