After more than two years of intensive and sometimes acrimonious study, U.S. and Canadian scientists have failed to reach agreement on the causes and effects of acid rain and on whether immediate steps should be taken to control damage to forests and fishing.

The conclusions of the scientific team, released yesterday in Ottawa, are likely to intensify the political battle between the two countries over acid rain. Canadian officials have accused the Reagan administration of "blatantly" manipulating the scientific team in an effort to forestall immediate action.

Acid rain occurs when air pollutants undergo chemical changes in the atmosphere and come back to Earth in rain and snow. It has been blamed for killing aquatic life in hundreds of lakes and rivers in eastern Canada and the northeastern United States. Canada contends that most of the pollutants come from the coal-fired power plants of the midwestern United States.

Diplomatic negotiations, initiated under the Carter administration, have been stalemated since last June. Acid-rain amendments to the Clean Air Act failed to clear Congress last year, and the legislation's leading Senate advocate recently told Canadians that it faces an "uncertain" future this year.

Canada, fearful of the possible effects on its $24 billion-a-year forest and fishing industries, has called for immediate action to reduce sulfur dioxide emissions, believed to be the main culprit in acid rain. The United States, equally fearful of the effect of expensive new pollution controls on the recession-pressed industries of the Midwest, has called for more research.

Both sides had counted on the bilateral team of scientists, working under a diplomatic agreement, to provide direction to diplomats and legislators.

But in their report, which was more than a year overdue, the scientists essentially agreed to disagree on several crucial points.

In its summary, the U.S. team acknowledged that "biological changes have occurred" in areas receiving acid rain, but it said that "cause-and-effect relationships have often not been clearly established."

In a separate summary, the Canadian team said that not only is there a clear relationship between acid rain and aquatic damage, but also that evidence shows that cutting sulfur dioxide emissions in half "I am unhappy about the delays in negotiations. Canada recognizes acid rain as a clear and present danger to the environment." would protect all but the most sensitive areas from further damage and "would lead to eventual recovery of those waters that have already been altered chemically or biologically."

In a statement released in Ottawa yesterday, John Roberts, Canada's minister of the environment, said that the Canadian team's conclusions support its last diplomatic proposal to the United States: a 50 percent cutback in sulfur dioxide emissions for both countries.

"I am unhappy about the delays in negotiations," Roberts said. "Canada recognizes acid rain as a clear and present danger to the environment . . . . I urge the U.S. to reconsider the proposal we have made."

Roberts said he would refer the final report to an international group of scientists and added, "I am confident that the peer review will support the conclusions drawn by Canadian scientists."

Canadian officials yesterday also complained that two other scientific panels working under a memo signed by Canada and the United States on Aug. 5, 1980, have not been operating. One of them was to explore the legal ramifications of acid-rain controls, and another was to propose ways to control emissions.

Most of what the Canadians want from the United States is embodied in Senate amendments to the Clean Air Act, which call for an 8-million-ton reduction in sulfur dioxide emissions over 12 years in 31 states east of and bordering the Mississippi River. But the Clean Air Act ended the year hopelessly mired in Congress, where many members are looking for ways to loosen restrictions, not tighten them.

In a speech to Canadian environmentalists this month, Sen. Robert T. Stafford (R-Vt.), chairman of the Senate Environment and Public Works Committee and a cosponsor of the acid-rain provisions, warned that "our proposal faces an uncertain reception" in Congress this year.

"Many politicians see acid rain control as an economic issue, rather than as an environmental issue," Stafford said, and he urged Canada to send a "strong and unmistakable signal" by taking steps on its own to cut sulfur dioxide emissions.

Meanwhile, in an effort to build grass-roots support for acid-rain controls, environmentalists have put the issue on the agenda in more than 180 town meetings in New Hampshire. New Hampshire town meetings are held March 8.

Proponents of acid-rain controls hope that focusing attention on acid rain in New Hampshire, which has suffered acid damage to its lakes, will publicize the issue as last year's town meetings did for the nuclear freeze movement.