President Reagan informed Congress yesterday that unless the Romanian government allows a significant increase in Jewish emigration it will be in "serious jeopardy" of losing the preferential trade status the United States granted it in 1975.

The warning was the strongest high-level U.S. criticism in recent years of the internal policies of President Nicolae Ceausescu's communist regime, which earned a special position in Washington in the 1970s because of its relatively independent foreign policy stands inside the Soviet bloc.

At the same time, a letter of protest to Ceausescu, now being circulated for signatures in the Senate by Daniel Patrick Moynihan (D-N.Y.), broadly attacked the Romanian government's treatment of ethnic and religious minorities in addition to Jews.

Citing documents and other information reaching the U.S. Helsinki commission, Amnesty International, Radio Free Europe and private organizations, the letter denounced what it called "ample use of prisons, labor camps and psychiatric facilities . . . in the apparent deliberate harassment of Baptists, Pentecostals, Orthodox and other religious groups."

The letter further charged that there has been a "remorseless dimunition of the educational and cultural facilities" for 2.5 million Hungarians living in Romania.

As of yesterday, 31 senators had signed the letter and a spokesman for Moynihan said the number could reach 50 within a few days.

Reagan's warning came in the form of a routine transmission to Congress recommending that "most favored nation" status be extended for another year to Romania, Hungary and the People's Republic of China. This status means in essence that tariffs on goods from these countries will be no higher than on goods from friendly countries.

Under an amendment to the 1974 Trade Reform Act, Congress can vote such concessions for communist countries only after a determination by the president that they have open emigration policies.

The president advised Congress that Hungary's emigration policies continued to reflect a "positive approach" and China was continuing a commitment to open emigration. However, Reagan said that Jewish emigration from Romania to Israel had dropped from a high of 4,000 persons a year to only 972 cases in 1981, with a backlog of at least 652 cases.

At the same time, the president said that the emigration process was "cumbersome and plagued with obstacles for those who merely wish to obtain application forms."

Sixty thousand Jews are estimated to live in Romania.

The strong language indicated a break on the part of the administration with a previous policy of tolerating political repression in Romania because of its independence on such issues as the Middle East and participation in Warsaw Pact military maneuvers.

In the early 1970s, Ceausescu gained a special relationship with the Nixon administration when he played the role of intermediary in the administration's early approaches to the People's Republic of China.

However, some members of the Reagan administration, centered in the National Security Council, now reportedly favor a tough line that would use economic pressure, such as the threat of withdrawing trade concessions, to force internal changes in Romania.

Romania is currently struggling to resolve serious financial problems resulting from heavy borrowing in the West, and is counting on the U.S. government to provide loans for commodity buying and other help. But administration hard-liners want to withhold any help pending political reforms