Cargill, Inc., the giant privately owned agribusiness conglomerate based in Minnetonka, Minn., made $5 million in "unusual payments" in the U.S. and in some 38 other countries in order to cultivate business.

The information was submitted earlier this month by the company to the Internal Revenue Service in answer to a questionnaire it sent to the country's biggest corporations. The IRS wants to determine, according to the questionaire, if "secret slush funds" were used for "corporate political contributions, lobbying, bribery, kickbacks . . . and if such payments were deducted from taxable incomes.

Many publicly owned companies have voluntarily admitted to making questionable or illegal payments in the U.S. and abroad to the Securities and Exchange Commission under a soon-to-be-ended moratorium from prosecution.

But since Cargill's stock is not held by the public, it is not subject to SEC jurisdiction. A Cargill spokesman said the company volunteered information on the payments, which were made between June 1971 and the end of last year, in answer to an inquiry from the Minneaplis Star. It published the information yesterday.

With annual sales estimated at $10 billion, Cargill is generally described as the country's biggest privately held company. Not far behind Cargill - and probably the No. 2 privately held company - is another agribusiness conglomerate, Continental Grain Co. of New York.

These companies, with agents and affiliates all over the world, are the leading grain exporters. They also deal in seeds, feeds, fertilizers, mining, metals, shipping, chemicals, financial services, and food processing.

Cargill's foreign trading arm, called Tradax, is based in Brussels and is the company's primary representative overseas.

According to Cargill, the payments totaled $16,969.75 in the U.S. and the rest in foreign countries. None of the domestic payments went to any federal, state, or municipal employee or involved any government contract, Cargill claimed.

It also said that none of the payments involved illegal political contributions. A Cargill spokesman said it was following the "IRS definition" of illlegal political contributions.

Cargill said it had ended the common practice in Spain of keeping two sets of books to avoid that country's taxes.

Payments to foreign officials by grain companies hava long been rumored. Representatives of the companies often sell the grain to countries through foreign officials. Their decisions can mean millions of dollars in profits to the grain sellers.

Edward W. Cook, chairman of Cook Industries of Memphis, the No. 3 grain exporter confided to the Barron's magazine in its Feb. 28 issue that he paid a $200,000 kickback to a foreign official. He said he made the payment because the life of a Cook agent had been threatened if the money was not paid.

Cook also said that this was the only kickback the company ever paid.

Cargill said it told the IRS that its internal audit was continuing and that it would report any further evidence of questionable payments.