Income reported by Japanese-owned companies operating in the United States declined 65 percent to $219 million in 1987, according to figures released yesterday, a fall that gives new ammunition to congressional critics who contend that many of the firms are manipulating their books to avoid paying U.S. taxes.

Income reported by all foreign-owned companies, however, rose to $5.6 billion from a net loss in 1986. Higher income normally results in higher tax being paid.

As foreign capital began streaming into the United States in the 1980s, the role of foreign firms in the economy began rising quickly. Their sales rose from $459 billion in 1984 to $650 billion in 1987, according to yesterday's figures.

The Internal Revenue Service is reported to be auditing in detail the U.S. operations of many foreign companies and banks.

Rep. Duncan Hunter (R-Calif.) and two other Republican members of the House yesterday released the figures, which were provided to them by the IRS, and charged that foreign companies may owe up to $50 billion in back taxes. They urged that any money due be collected before U.S. citizens are asked to pay additional taxes as part of a new budget package.

The Organization for Fair Treatment of International Investment, which represents foreign investors, concedes that income reported in 1986 by foreign companies fell sharply. But it says that was due to hard times and the impact of a falling dollar, which is hard on the companies because they import a lot of goods.

"In '86 our tax went down because our income went down," said Sandra E. Taylor, chairman of the group's Washington committee. "It wasn't because we were manipulating" the books. She noted that total income reported rose in 1987, calling it an end to the temporary conditions of 1986.

She suggested that the income of Japanese companies as a group may have continued to fall in 1987 because of heavy costs associated with starting up new U.S. plants, particularly auto factories. Japanese-owned companies had reported total sales of $185 billion and profit of $219 million.

Critics charge that foreign companies may be illegally inflating costs at their U.S. subsidiaries to lower profit reported here and U.S. taxes paid. In this way, profits are said to be transferred to appear on the books of the parent company or some subsidiary in another country.

Hunter yesterday also released a letter from a former American employee of Sony Corp. of America. The employee said he had questioned certain "service charges" that his employer was carrying on its books. In the letter, the man said he was told to destroy copies of a memo he had written on the subject and soon after was fired on "trumped-up charges."

Sony spokesman Jason Farrow said yesterday that "it's Sony's corporate policy to obey U.S. law and we conscientiously strive to do that." Farrow denied the allegation of misconduct and said the employee was dismissed for "just cause" in June 1989 and had brought a legal action against the firm.