After considerable debate, Congress has sent President Reagan a bill that would require the Veterans Administration to pay disability benefits to veterans suffering from two health problems that may stem from exposure to the herbicide Agent Orange.

It marks the first time the government has acknowledged that exposure to Agent Orange might have harmed troops. Since 1971, when the military stopped using it to kill crops and clear jungle in Vietnam, the government had insisted that there was no proof that the herbicide caused health problems.

The measure also calls on the VA to prepare a plan for compensating veterans who were exposed to atomic radiation during military tests or the occupation of Hiroshima and Nagasaki.

The bill requires the VA to pay disability benefits, at least temporarily, to veterans who prove that they developed chloracne, a skin condition, or prophyria cutanea tarda (PCT), a liver ailment, within one year after they left Vietnam.

Benefits will be paid from Oct. 1, 1984, until Sept. 30, 1986, by which time several federal studies will have been completed and the government says it will have determined whether the two illnesses are linked to Agent Orange.

Within 300 days after the legislation is signed, VA Administrator Harry N. Walters must publish final regulations that explain how the agency will resolve all Agent Orange claims, including those for chloracne and PCT. The bill also would create an independent scientific panel to advise the VA about what diseases, if any, should be recognized in the future as being linked to herbicides or atomic radiation.

For several years, Rep. Thomas A. Daschle (D-S.D.) and others have introduced Agent Orange compensation legislation, but the measures never made it out of the House Veterans' Affairs Committee, which insisted that there was insufficient scientific proof of a link.

Pressure on the House began to build in late 1982, however, when the Veterans of Foreign Wars threw its weight behind Daschle's bill. A few months later, the American Legion made a similar move.

Since neither group cited any scientific reason to explain why it suddenly favored compensation, it was widely believed that they were bowing to pressure from members who were Vietnam veterans or that they hoped to attract new members from the Vietnam war era.

The House committee, finding itself on the opposite side of legislation endorsed by groups representing 5 million veterans, responded by passing a scaled-down version of Daschle's bill. The measure would have required the VA to compensate veterans suffering from soft-tissue cancers and the other two diseases, even though "there is insufficient medical evidence to conclude that such diseases are service-connected."

However, Sens. Alan K. Simpson (R-Wyo.) and Alan Cranston (D-Calif.), the chairman and ranking minority member of the Senate Veterans' Affairs Committee, refused to bow to the veterans' groups. They wrote a bill that called for a new science advisory committee and would have required the VA to adopt uniform procedures for deciding how it would resolve Agent Orange claims.

Eventually, both chambers compromised on the bill's final version. It comes after two government studies have found no link between health problems cited by veterans and exposure to Agent Orange. MORE ON OUTSIDE FEES . . .

VA Chief Walters has approved the firing of Dr. Rocco P. Sciubba, 64, a physician at the VA medical center in Coatesville, Pa., who admitted that he had violated VA regulations by operating a private practice in his home. The VA seldom fires doctors and the case caused a stir because most of Sciubba's patients were mentally retarded youngsters who attended a school run by his church.

Sciubba contended that the VA operates under a double standard because it allows high-ranking doctors to earn outside incomes by teaching or consulting.