The Justice Department yesterday contended in federal court that a McDonnell Douglas Corp. executive received kickbacks from a Pakistani businessman who allegedly received secret commissions on the sale of DC10 jetliners.

But Sherman Pruitt Jr., the executive, pleaded innocent yesterday to two counts of making false statements to a federal grand jury which was investigating his firm's overseas sales activities.

It was the first time during a three-year Justice Department-Customs Service investigation of overseas bribes that the government has alleged an American corporate official took money allegedly paid of foreign agents.

At a hearing in U.S. District Court here, Justice Department lawyer George J. Mendelson said the alleged payments to Pruitt were deposited in two Swiss bank accounts. Records obtained by the government showed over $50,000 in secuirties and cash in those accounts, Mendelson told Judge Joyce Hens Green.

The perjury indictment charged that Pruitt, who was sales manager for a McDonnell Douglas subsidiary, falsely stated he had no foreign bank accounts and that he did not disclose full information about alleged payouts by Leslie Sequeira, a Parkistani businessman.

Mendelson told Green yesterday that the government contends Pruitt received kickbacks from Sequeira.

Investigators have believed for some time that American corporate officials received cuts of some of the commissions paid foreign agents. The records obtained from the Swiss bank accounts in the Pruitt case were the first time that investigators obtained evidence to support their suspicions.

The government obtained the bank account records through a 1973 treaty with the Swiss government, which provides for disclosure if the U.S. government can show that a possible crime has been committed.

Four McDonnell Douglas executives, including Pruitt, were indicted in November on charges they made $1.6 million in secret "commission" payments on the sale of DC10 aircraft to Pakistan. According to the indictment, McDonnell officials, and coconspirators in Pakistan agreed to add $500,000 to the price of four DC10s to cover the commission costs. The jetliners were bought by the government-owned Pakistan International Airlines.

McDonnell Douglas officials have denied all the charges. Green has scheduled a trial in the case for June. She said yesterday the perjury charges against Pruitt would be tried 45 days after the main trial.