Three of the highest-ranking advisers to departed Environmental Protection Agency administrator Anne M. Burford will resign today as the White House begins the final housecleaning of the troubled agency, administration officials said last night.

Acting Administrator John W. Hernandez Jr., general counsel Robert M. Perry and Assistant Administrator John A. Todhunter, all under fire from congressional subcommittees probing allegations of wrongdoing in the agency, will announce plans to leave the agency, and others are expected to follow, the officials said.

William D. Ruckelshaus has been named by President Reagan to become the next EPA administrator, but administration sources have said that his Senate confirmation could take a month or longer, and the White House is anxious to replace Hernandez with another acting administrator as soon as possible.

"They want the odor to dissipate before Ruckelshaus arrives," one administration official said.

Hernandez has been criticized repeatedly in recent days for allowing Dow Chemical Co. to suggest changes in a report that largely blamed the chemical company for serious dioxin contamination in Michigan. Hernandez came under fire again yesterday at a hearing where it was revealed that he blocked for 20 months a cleanup of dangerous lead contamination in a poor, black neighborhood in Dallas.

Todhunter also has been accused of ordering changes in the Dow report and of holding private meetings with industry groups before declining to restrict the use of formaldehyde and other potential cancer-causing substances.

Perry is under investigation for possible perjury in congressional testimony on whether he compiled negative information about certain EPA employes.

Subcommittees also are examining whether Perry violated conflict-of-interest laws by participating in the settlement for cleanup of the Chem-Dyne hazardous waste dump in Hamilton, Ohio, where a subsidiary of Exxon Corp., Perry's former employer, deposited toxic wastes and was a potential defendant in the case.

All three have denied all charges of wrongdoing.

Lee Verstandig, one of several acting EPA officials appointed by the White House last month at the outset of the controversy, is expected to be named acting administrator until Ruckelshaus is confirmed by the Senate. For the last month, Verstandig, a former assistant secretary of transportation and former associate dean at Brown University, has been in charge of congressional relations for the agency.

The three resignations will bring to 11 the number of political appointees who have left the EPA since Feb. 7, when Reagan fired hazardous waste cleanup chief Rita M. Lavelle, an action setting off a series of investigations that ultimately prompted Burford to resign two weeks ago. The changes will leave four of the EPA's six divisions under the command of temporary appointees.

Ruckleshaus spent the first half of the week in Washington and was kept abreast of plans to remove the most controversial of Reagan's first generation of EPA appointees. Others are expected to resign soon, some of them under pressure.

Federal security police were dispatched to the offices of the departing officials, according to EPA sources, to make certain that no sensitive documents that could be needed in the continuing congressional investigation are removed.

Meanwhile, witnesses told a House public works subcommittee yesterday that Hernandez blocked the cleanup of a poor Dallas neighborhood, even though one of the responsible companies had agreed to begin to correct the situation.

Three top officials from EPA's Dallas regional office said they disagreed with but could not overturn Hernandez' order that more health tests be conducted before three lead-smelting companies could be forced to clean up the lead-contaminated soil in schoolyards, day-care centers and playgrounds near the plants.

Patricia Spears, who lives with her four children eight blocks from one of the Dallas smelters, said her family and others have already suffered symptoms of lead poisoning.

"My oldest son, 14, has been in and out of doctors' offices and hospitals since he was 3. He has been diagnosed with a learning disability. He has blackouts, chest pains, leg aches, severe headaches, stomach pains to the point where it would double him up in pain . . . . I'm at a point now where my 8-year-old, my baby, has a limp now . . . and she's fallen back in a lot of her school subjects," she said.

Spears said that although her family and many neighbors had experienced health problems for years, it was not until tests were conducted in 1981 that she realized the problems might be related to lead. She said many of her neighbors are afraid to go outside in their yards now because of the contamination.

Lead in sufficient quantities is known to cause brain damage in children.

Frances Phillips, deputy administrator of the Dallas EPA office, said her office had prepared a news release announcing the cleanup when Hernandez ordered further testing instead. Since that time, the company, RSR Corp., has done some voluntary cleanup. During congressional testimony last week under oath, Hernandez denied knowing any of the firms had agreed to pay for their own cleanup.

Phillips said that although testing in the area had shown abnormal lead levels in children, Hernandez could not be convinced of an immediate problem. He also objected to a determination by Dallas EPA scientists that the initial cleanup should cut back lead levels to no more than 1,000 parts per million.

"He said he didn't think we should spend any money to remove dirt or start any bulldozers until we could identify the specifics of the health problems of this case," she said.

Phillips said she called Hernandez back to try to change his mind. "I reminded him this was in a poor area of Dallas and that the region was concerned about the children."

She said she also complained that Hernandez was changing the usual EPA standard of proving a "potential health problem to having to prove an actual health problem" before cleanup could begin.