The Japanese government yesterday issued its automakers individual quotas on exports to the United States, triggering immediate warnings from imported-car dealers here that there could be a shortage of Japanese cars as early as next month.

The quotas were in line with Japan's agreement last month, in response to pressure from the Reagan administration, that it would "voluntarily" limit the exportation of Japanese cars here to 1.68 million units this year, compared with 1.82 million shipped last year. The quotas are effective for the year beginning last April 1.

Japan's Ministry of International Trade and Industry, which individually called in representatives of the seven automakers to announce the quotas, refused to reveal the individual limits given each company. Ministry officials said the quotas were based on shipments here during 1979 and 1980, but smaller automakers were given "special consideration" because they haven't yet established themselves in the U.S. market.

Press reports emanating from Japan, however, estimated the quotas would be: Toyota 518,000, down from 563,000 last year; Nissan, maker of Datsun cars, 456,000, down from 500,000; Honda, 347,000, down from 372,000; Toyo Kogyo, maker of Mazda cars, 159,000, down from 174,000; Mitsubishi, 114,000, down from 125,000; Fuji Heavy Industries (Subaru), 70,000, down from 81,000 and 17,000, up from 3,000, for Isuzu Motors, which is partly owned by General Motors.

Spokesmen for the Commerce Department and U.S. Trade Representative said they had no official knowledge of the quotas.

Robert M. McElwaine, president of the American International Automobile Dealers Association, yesterday predicted the new quotas could result in shortages of small, fuel-injected Japanese cars by the end of July. Japanese car sales for April, May and June, the first three months of the quotas, have been brisk, McElwaine said, so shipments here for the rest of the year will have to be cut back drastically.

Sales last month were particularly good, McElwaine said. Sales of all imports rose from 197,200 during May last year to 209,273. About 75 percent of the autos sold were from Japan, he said. "There was a flurry of sales soon after the cutback was announced" last month, McElwaine said.

The sharp decline in imports will result in fewer cars on the lots, customers paying full prices or more and getting lower trade-in allowances, McElwaine said. Although car prices from dealers will be higher as a result of the shortage, he said the prices set in Japan will probably be kept low because of the strength of the dollar against the yen, which makes imports cheaper here.

McElwaine also said he expects a larger proportion of higher-priced luxury Japanese cars, which provide dealers more profit per vehicle. "It would go against the grain of corporate finance for them not to try to maximize their profits," McElwaine said.

Officials of Toyota, Nissan and Honda have said, however, they are reluctant to reduce their shipments of economy cars such as the Toyota Corolla, Datsun 210 and Honda Civic in favor of high-profit luxury cars such as the Datsun Maxima and Toyota Cressida, McElwaine said. They fear losing their foothold in the American economy-car market. Dealers here will probably be sold cars by the manufacturers based on their past sales performance, he added.

U.S. Trade Representative William E. Brock has said the restrictions will not mean higher prices on foreign or domestic autos or a scarcity of Japanese imports.

Toyota Motor Co. expressed "strong dissatisfaction" with the extra allowances for small manufacturers and apparent disregard of its suggestion that quotas be based strictly on export records. Nissan called the quotas "extremely regrettable."

Brock announced the limitation plan during a visit to Japan in May. He warned high-ranking Japanese officials that if they didn't voluntarily restrict automobile exports here, Congress would do it for them.

The Japanese government said it would reduce its exports the first year by 7.7 percent, increase shipments in the second year according to the growth of the U.S. market, and in the third year would consider whether further restraint was necessary.