The head of the J. Roderick MacArthur Foundation, which pays out millions of dollars each year to civil liberties and human rights groups worldwide, sued the FBI in federal court here yesterday for keeping secret records on his, and the foundation's, activities.

In a complaint filed by the American Civil Liberties Union, the Chicago-based foundation's president, Lance E. Lindblom, charged that maintenance of the files is a violation of their constitutional and privacy rights and has had a chilling effect on their activities.

The FBI has released only a small portion of the records to Lindblom under the Freedom of Information Act, blacking out most of the documents primarily on national security grounds. The bureau also told Lindblom in a 1989 letter that the records "contain information furnished by another government" agency or agencies.

Lindblom said the documents he has been given include references to a February 1985 trip he made to South Korea as a member of an American human rights group that accompanied political opposition leader Kim Dae Jung to Seoul after two years of exile in the United States.

Members of the delegation were roughed up at the Seoul airport by South Korean police who forcibly separated them from Kim, punched him as he was put into an elevator, and placed him under house arrest.

Lindblom said in an interview yesterday that he believes the FBI investigative file, apparently totaling fewer than 50 heavily censored pages, was started then. The FBI has said it has no file on the foundation as such but has other records in which the foundation is mentioned.

Lindblom said he first asked for the papers in 1988 after hearing that the bureau had files on some other foundations. More than half of the foundation's work is international, including grants for human rights monitoring to various groups, while its domestic work focuses heavily on First Amendment issues. Lindblom said grants this year will total between $2.2 million and $2.3 million.

As a result, Lindblom said in his petition, he meets "high foreign officials who are involved in human rights, political, social and economic issues" as well as people who "sometimes support causes that are contrary to official U.S. foreign policy."

His lawyers said the FBI has no basis for believing that Lindblom or the foundation "was engaged in any unlawful or national security related activity" and that the maintenance of secret files "prevents and chills" other individuals and organizations from dealing or freely communicating with them.

An FBI spokesman declined to comment, saying it would be "inappropriate" now that the matter is in the courts. The case was assigned to U.S. District Judge Thomas Penfield Jackson.