WASHINGTON, Nov. 14, 1986 — President Reagan today signed a comprehensive health bill designed to promote exports of prescription drugs and to compensate children injured by vaccines.

Mr. Reagan said he had approved the bill ”with mixed feelings” because he had ”serious reservations” about the vaccine compensation program.

But he warmly endorsed provisions of the bill that would, for the first time, allow pharmaceutical companies to export drugs to other countries that have approved their use, without waiting for the United States to approve the drugs’ sale here. Mr. Reagan said this part of the new law ”will increase the competitiveness of the American pharmaceutical industry abroad, create jobs, foster biotechnology and aid other nations.” Separation-of-Powers Issue

However, he said there were ”substantial deficiencies” in the vaccine plan, under which injured people could obtain payments from the Government without proving fault or wrongdoing by the vaccine manufacturer or anyone else.

The program would be ”administered not by the executive branch, but by the Federal judiciary,” Mr. Reagan said, calling it an ”unprecedented arrangement” that was inconsistent with the constitutional requirement for separation of powers among the branches of the Federal Government.

Mr. Reagan’s action came after heavy lobbying in favor of the bill by a broad-based coalition including drug companies, physicians and groups representing children and the elderly. Agency Had Urged Veto

The Justice Department had urged a veto of the bill because of its objections to the new system of compensating people injured by vaccines. But Vice President Bush, Commerce Secretary Malcolm Baldrige and Dr. Otis R. Bowen, Secretary of Health and Human Services, urged Mr. Reagan to sign it, as did James A. Baker 3d, Secretary of the Treasury.

The compensation program would be financed by a new excise tax imposed on each dose of the vaccines for poliomyelitis, diphtheria, whooping cough, tetanus, measles, mumps and rubella. But Congress adjourned this year before it could actually establish the tax, and the compensation program will not take effect until it does so.

Representative Henry A. Waxman, a California Democrat who drafted the portion of the bill relating to vaccines, said he expected Congress to establish the tax ”as quickly as possible next year.”

Mr. Reagan said he hoped that Congress, in adopting any excise tax, would also make ”corrective” changes in the framework of the vaccine program to address his objections.

Under the program, people would file claims in a Federal District Court. The judge would appoint a special master to determine the appropriate amount of compensation to be paid from a special Government trust fund, under guidelines set by the new law. The judge could revise the amount.

Parents of the injured child could accept the award as full payment, or they could reject it and file a lawsuit against the manufacturer. The new law sets certain limits on the manufacturer’s liability in such lawsuits. A Congressional report said one purpose was ”to lessen the number of lawsuits against manufacturers” while compensating victims of vaccine injuries. High Costs of Insurance

In recent years the number of such lawsuits has increased, and the prices of vaccines have risen rapidly. The increase in the cost of liability insurance and the unpredictable nature of such liability have forced some manufacturers to consider abandoning production of vaccines, even though the vaccines have been highly effective in protecting millions of children against disease.

Under the new law, drugs not approved by the United States Government could be exported to any of 21 foreign countries if they were approved for use there. The countries, limited to those with government agencies that review the safety and effectiveness of drugs, include Austria, Britain, Canada, France, Italy, Japan and West Germany.

Other countries often approve new drugs more quickly than the United States. The bill ran into some opposition from those who said it would be setting a double standard on the safety and effectiveness of drugs, but proponents countered that it was arrogant of the United States to tell another country it could not have a medicine it wanted just because an American agency had not got around to approving it.

The bill, passed with bipartisan support Oct. 18, the last day of the 99th Congress, applies only to drugs for which manufacturers are in the process of seeking approval from the Food and Drug Administration A drug may not be exported if the agency has disapproved it for sale in the United States. Other Provisions of Bill

The bill would also require states to provide medical and psychiatric care, housing and employment services for people who are chronically mentally ill, including homeless people.

Another section of the new law, designed to reduce medical malpractice, will make it easier for physicians to take disciplinary action against their colleagues. The measure makes clear that such actions do not violate antitrust laws.

Under the health bill, the Secretary of Health and Human Services must arrange for a national computer file to record information about malpractice claims and disciplinary proceedings. Hospitals would have to consult the file before permitting doctors to practice at their facilities.

The law also establishes a national commission to recommend ways of reducing infant mortality. It provides $14 million a year for research on Alzheimer’s disease. And it ends Federal authority for the national health planning program begun in the 1970’s.

Mr. Reagan said the program, which set up a network of state and local health planning agencies, had been ”detrimental to the rational allocation of economic resources for health care.” States may continue to finance the work of such agencies, which review the need for construction of hospitals and nursing homes, purchases of major medical equipment, and the addition of such services as open-heart surgery.

Senator Orrin G. Hatch, Republican of Utah, said Mr. Reagan had shown ”wisdom and compassion” in signing the bill. Senator Edward M. Kennedy, Democrat of Massachusetts, a co-sponsor of the legislation, said he, too, was ”delighted.”

Gerald J. Mossinghoff, the president of the Pharmaceutical Manufacturers Association, said the new law ”greatly strengthens the ability of the United States pharmaceutical industry to compete in international markets.” Richard D. Godown, the president of the Industrial Biotechnology Association, also applauded the President for signing the bill.