The Spanish Airline Iberia yesterday filed a multi-million dollar lawsuit against The Boeing Company contending that the big aircraft manufacturer made more than $3.5 million in secret payments to a Madrid agent as commissions on the sale of 29 jet aircraft to Iberia in 1971.

Iberia said in papers filed in U.S. District Court that prior to the sale, Boeing falsely assured Iberia officials that it had terminated the commission agreement and would adjust the final sale price on the aircraft accordingly.

Instead, Iberia contended in the lawsuit, Boeing made other payment agreements with the Madrid agent that would be "substantially equal" to the amount of the cancelled commissions. Iberia alleged that the payments were made to the agent's account at the First National City Bank in New York and transferred to banks in Switzerland and elsewhere.

Iberia said in its lawsuit that it had information that the payments were made to Fulgencio Amador Moreno, a Madrid business agent, his family and associates or to a corporation there owned by Amador.

As a result of Boeing's allegedly false representations, Iberia contended that it went ahead with the aircraft purchase for a total of $231 million, $98 million of which was borrowed from The Export-Import Bank of the United States in Washington. Boeing assisted Iberia in obtaining the loans, the lawsuit said, but falsely told the bank that no sales commissions were being paid.

As a result of the alleged misrepresentation, Iberia contends the bank could now demand the unpaid portion of the loan, which totalled $87.7 million as of last October.

In July 1978, the Securities and Exchange Commission charged that Boeing had made at least $52 million in secret payments to various foreign government officials and businessmen as commissions for overseas aircraft sales.

Boeing neither admitted nor denied the payments but signed a consent order detailing some of the transactions. Disclosures filed with the SEC named various countries, many in the Middle East, where commission arrangements were made, Iberia said in its lawsuit. The report to the SEC listed a transaction in an unidentified country, which Iberia contends was the commission paid for its purchase of the jet aircraft, the lawsuit said.

A spokesman for Boeing said the company believes the lawsuit "stems from a misunderstanding of the transaction in question."