The White House has begun a subcabinet shakeup by signaling dissatisfaction with several presidential appointees, one of whom resigned this week from a top post in the Energy Department.

Robert E. Thorne, the assistant secretary for energy technology and a veteran of government energy jobs, submitted his resignation to the White House Thursday after being asked to resign by Energy Secretary James R. Schlesinger Jr.

Others who have so far received what was called a "negative rating" from the White House include two top Labor Department officials, Undersecretary Robert J. Brown and Francis X. Burkhardt, assistant secretary for labor-management relations.

Sources said Labor Secretary Ray Marshall has talked with both men but has taken no formal action as yet. They said he is scheduled to meet with presidential aide Hamilton Jordan on Monday to discuss the future of Brown and Burkhardt, neither of whom has resigned.

Administration sources said Commerce Undersecretary Sidney Harman, who submitted his resignation recently, also had received an unfavorable rating. Harman, however, adamantly has denied that he resigned under pressure, saying two White House aides told him he had been doing a good job.

The shakeup stems from a months-long "assessment" by the White House of sub-cabinet appointees, aimed in part at regaining some control over departmental machinery that was surrendered at the start of the administration when it espoused the principle of "cabinet government."

When the review began in earnest last summer, officials said it was designed to weed out those found to be lacking in performance, loyalty or both.

Department heads were asked to assess their deputies and assistants and forward the results to the White House, where senior presidential aides then compiled their own assessments in consultation with the Office of Management and Budget, according to one source. Reviews have been completed thus far for the departments of Justice, Commerce, Labor and Energy, this source said.

Brown and Burkhardt reportedly were faulted for poor performance. But labor union sources have expressed other suspicions, noting that the two men were the most prominent appointees from the union movement in the Labor Department.

"why pick on the two people who come out of the labor movement?" asked a spokesman for the United Auto Workers. "There's plenty else wrong with government... what it seems to be is a general attitude that labor doesn't count anymore."

Brown was a local United Auto Workers president in Minnesota before joining the Labor Department in 1966. Burkhardt came out of the painters' union, an AFL-CIO affiliate.

At the Democratic Party midterm conference in Memphis, presidential assistant Tim Kraft, whose office is conducting the review of sub-cabinet officials, said last night: "I am aware generally of the review, but I am not going to comment on individuals.

Kraft did not deny that the two Labor Department officials had received "unsatisfactory" ratings from the White House or that their status is in doubt.

As for the Energy Department, one administration official said Thorne's resignation may not be the end of an overall campaign to improve the management and performance of the agency created by Carter at the start of his administration.

"More heads will fall," the official predicted. Schlesinger himself often has been rumored as about to leave the 20,000-member department, and there has been speculation in recent months of major personnel changes.

Thorne "just couldn't whip it into shape," said a senior DOE official, speaking of Thorne's control of one of the department's most critical offices, which includes nearly $5 billion in spending for solar, nuclear and fossil fuel development technology.

Thorne is expected to be replaced by John M. Deutsch, a former Massachusetts Institute of Technology chemistry professor who has won high marks from the White House and Congress since being named last year to head the department's office of energy research.

One irony in Thorne's forced resignation is that the Environmental Policy Center, a public advocacy group that opposed his appointment and held it up for months, now regrets his departure. EPC's Janet Hieber yesterday praised Thorne's support for renewable energy technology and conservation.

Thorne declined to take calls from reporters yesterday and was scheduled to leave for Paris today to attend an International Energy Agency meeting.