Justin Dart Jr., commissioner of rehabilitation services at the Education Department, has been forced to resign in a dispute with Madeleine C. Will, assistant education secretary for special education and rehabilitative services.

Dart, who was appointed by President Reagan in September 1986, has been embroiled in a longstanding disagreement with Will, who he said usurped his authority to manage the Rehabilitation Services Administration, which oversees programs aimed at helping disabled adults become self-sufficient.

Dart is the son of the late Justin Dart, entrepreneur and member of Reagan's original "kitchen cabinet." The younger Dart previously was a presidential appointee to the National Council on the Handicapped.

Dart said yesterday that department officials asked him to resign last week and that he had submitted a letter of resignation to the White House.

"I have had significant differences of opinion in regard to management," he said yesterday. "The major issue . . . is the civil and human right of disabled people to have more than a rubber-stamp figurehead representation in the government."

At a hearing Nov. 18 before the House subcommittee on select education, Dart, who is disabled, testified that the office headed by Will was afflicted with "profound problems in areas such as management, personnel and resource utilization. We are ravaged by disunity, and hostility internally . . . . "

Dart has said he was unable to hire personnel and make other management decisions. He said that on one occasion he had been forced to secure Will's permission to mail a Federal Express envelope.

Will could not be reached for comment yesterday, but William Kristol, chief of staff to Education Secretary William J. Bennett, disputed Dart's testimony.

"Justin was not used . . . to the rules and regulations in government that everyone has to abide by, and this frustrated him," Kristol said. ". . . He was in disagreement with the policies of the assistant secretary and with the secretary."

Rep. Major R. Owens (D-N.Y.), who chaired the hearings on rehabilitation services last month, said Dart's resignation was "the case of a high-level executive whistle-blower being kicked out.".