A new showdown is in the offing between the U.S. Congress and the United Nations, precipitated by the secretary general's apparent willingness to grant the Soviet Union yet another exemption to rules that govern other member states.

For decades, the Soviet Union has enjoyed some special privileges at the U.N. It has three representatives and three votes, instead of the one possessed by all other countries. And it is permitted to control Soviet nationals employed by the U.N. Secretariat through a practice called ''secondment'' that is accepted even though it is a clear violation of the U.N.'s charter and personnel rules.

How the U.N. came to accept Byelorussia and the Ukraine as ''independent'' member states when they are no more independent than Illinois and Indiana is a long, sad story that says much about how Western eagerness to have the Soviets join the United Nations led to a clearly absurd ''compromise.''

Less is known about how and why successive secretaries general of the United Nations accepted the Soviet violation of the concept of an international civil service. But certain facts are clear: Article 100 of the United Nations charter states: ''In their performance of their duties, the secretary general and the staff shall not seek or receive instructions from any government or from any other authority external to the Organization.''

However, early on, this provision, designed to ensure that U.N. employees would be independent of their own governments, was tacitly disregarded for Soviet and Soviet-bloc nationals in favor of the practice of ''seconding,'' which ensures the dependence of these nationals on their own governments. The result is precisely the opposite of the U.N. bureaucracy of international civil servants foreseen by the charter. ''Seconding'' ensures that Soviet nationals never become international civil servants.

Unlike other U.N. employees, Soviet and Soviet-bloc nationals working in the U.N. Secretariat remain employees of their own government, lent or ''seconded'' to the Secretariat for the duration of their U.N. employment (which is strictly limited by a ''fixed-term'' contract). Soviet nationals are rotated frequently, are required to live in a Soviet housing compound, take part in political indoctrination sessions and kick back their U.N. salaries to Moscow. The practice is a clear violation of both the letter and spirit of Article 100. For a long time, the practice of ''seconding'' has been deeply offensive to the U.S. government, not only because it violates the U.N. charter but because U.S. counterintelligence agencies believe that one-fourth to one-third of Soviet nationals ''seconded'' to the Secretariat are Soviet intelligence agents who use U.N. employment to gain entry and access to the United States and to other member states. No one justifies the ''secondment'' practice -- they just don't talk about it.

Last year, however, when a funding crisis drove the United Nations to the brink of collapse, reforms were adopted which promised to correct or at least ameliorate the situation. A hiring freeze was imposed by the secretary general and extended through 1987. The freeze was expected to reduce U.N. personnel by 15 percent over a three-year period. It also should have helped bring Soviet personnel practices into harmony with those of other member states because it confronted the Soviet government with the choice of either granting nationals indefinite extensions of their ''fixed terms'' or losing the positions.

One thing was utterly clear: short fixed-term rotation was incompatible with the secretary general's ''no replacement'' rule. The attack on ''seconding'' was further strengthened when the U.N.'s own ''wise men,'' the Group of 18, decreed that no more than 50 percent of the nationals of any country could be on fixed-term contracts. Currently, 100 percent of Soviet and Soviet-bloc nationals are ''seconded.'' Moreover, the General Assembly adopted resolutions reiterating that ''no post should be considered the exclusive preserve of any member state or group of member states.''

Neither the hiring freeze nor the Group of 18's resolutions would reduce the number of Soviets employed in the Secretariat. That number is reasonable and in keeping with general standards. But the new rules proposed by the Group of 18 would bring at least half of the Soviet and Soviet-bloc nationals under personnel policies applied to other U.N. employees.

Americans who expected the secretary general to enforce his own rules were disappointed when news leaked this month of a letter from Secretary General Javier Perez de Cuellar to the U.S. Department of State. In that letter, it is reported that Perez de Cuellar informed Deputy Secretary of State John Whitehead that, after conversations with Soviet Deputy Foreign Minister Alexander A. Bessmertnykh, he was considering granting 104 Soviet ''exceptions'' to the hiring freeze in order to replace current Soviet-bloc staff members who would be ''rotated'' out of the Secretariat.

When Sen. Robert Kasten (R-Wis.) learned of the letter from his own U.N. sources, he went public with the issue and said he was, in his own word, ''outraged'' -- so outraged that he announced on May 26 he would seek to block U.S. funds for the United Nations. ''This is an issue of extreme importance in the conduct of our foreign policy which I and most Americans will consider an outrage,'' Kasten said in a speech to the Senate. ''It is only through holding up funding that the United States can keep on track what is left of the U.N. reform movement.''

The secretary general, Kasten asserted, had not even informed the U.S. government of his decision ''until he learned that his secret deal was known by administration officials.''

Both Kasten and the State Department believe the proposed ''exceptions'' to the hiring freeze mark the end of a serious effort at fiscal and administrative reform in the U.N., and both have so informed the secretary general. Kasten believes the secretary general has already capitulated to Soviet demands and therefore, the senator says, U.S. funding should be contingent on the reversal of the policy of ''secondment.''

The secretary general, through a spokesman, has denied a ''deal'' and has asserted his determination not to be pressured by ''either superpower.''

An interesting confrontation looms.