Charges that a South African diplomat intruded into American politics by criticizing Sen. Dick Clark (D-Iowa) in his home state last week produced a formal inquiry by the State Department yesterday.

At an unusually senior level to underscore the seriousness of the accusation, Under Secretary of State David D. Newsom last night summoned South African Embassy Minister Willem Retief to receive the American complaint.

The accusation, aird in the Iowa press starting last Tuesday, is that South African Embassy Minister for Economics Jan H. Van Rooyen meddled in U.S. politics by criticizing Clark. The senator is chairman of the Senate Foreign Relations suncommittee on Africa, and he is up for reelection this year. Three Republican challengers are assailing Clark's views in championing black majority rights in southern Africa's racial conflicts.

Retief, the new No. 2 official at the embassy, was called to the State Department because Ambassador Donald B. Sole temporarily was out of town. Last week, Sole was called to the Department for an expression of American alarm that South Africa's paratroop raid into Angola to attack black guerilla bases there jeopardized western diplomacy for a peace settlement in the South African-ruled territory of Namibia (Southwest Africa).

A State Department spokesman said lst night that Newsom "made clear his concern that if the statements attributed to Minister Van Rooyen in Iowa had been accurately reported, that we would consider this to be an unwarranted intervention into a domestiv American political matter."

The spokesman said Retief responded that he would convey the complaint to his government.

On May 4 the Cedar Rapids Gazette reported that Van Rooyen was "asking lowans why their senator finds South Africa such a fine platform rather than dealing with the real problems this state might have."

The South African envoy was reported to have been invited to Iowa by a Republican state senator, Stephen Bisenius of Cascade, "to enhance trade." But Van Rooyen was quoted as having told a Gazette reporter that Clark was urging American firms doing business in South Africa to pull out of that country. Yesterday, The Des Moines Register editorially charged Van Rooyen with violating "One of the most basic laws of diplomatic protocol."

In the ensuing controversy, Van Rooyen and Bisenius said Van Rooyen did not volunteer any political views, but only responded to questions from the Gazette reporter. Van Rooyen insisted he did not criticize Clark in his meetings with Iowa trade officials. In turn, Clark said that he did not advocate the "extreme" trade pullout described by Van Rooyen, but favored "discouraging any new U.S. investment in South Africa" and encouraging U.S. firms to be "more responsive to the situation blacks in South Africa face."

Clark said last night, however, that "I certainly didn't request" the protest to South Africa. A State spokesman said "we decided on our part that it would be appropriate to have this (Newsom-Retief) meeting.