Secretary of Commerce Juanita Kreps ordered the Maritime Administration yesterday to sever its formal ties with the private National Maritime Council in light of the council's questionable lobbying and promotional activities.

Kreps announced that her decision to end the 7-year-old relationship, which constituted a formal alliance of business, labor and government in maritime affairs, was effective immediately.

A House Government Operations subcommittee headed by Rep. Benjamin S. Rosenthal (D-N.Y.) last week challenged the legality of the council's efforts to generate congressional support for the maritime industry last year during the controversial drive for "cargo preference" legislation.

The subcommittee disclosed at the same time a questionable pattern of promotional appearances by Maritime Administration officials at NMC dinner dances. The inquiry also turned up documents showing that the alliance was established in 1971 despite warnings from Commerce Department Lawyers that "the potential conflicts and embarrassment are too great."

The Maritime Administration, the government agency that gives out hundreds of millions of dollars a year in shipbuilding and operating subsidies, runs the day-to-day affairs of the Maritime Council, collects its dues and performs other services for it. The head of the Maritime Administration, Assistant Secretary of Commerce Robert J. Blackwell, is a member of the nonprofit council's board of governors.

Rosenthal welcomed the announcement, but made it clear that he considered further action essential.

"This is a necessary first step," Rosenthal said."Secretary Kreps is to be commended . . . but much more needs to be done to end the incestuous relationship that has existed between the Maritime Administration of the Department of Commerce and the National Maritime Council."

He said his subcommittee would "continue to carry out its oversight functions regarding the Maritime Administration already has asked the General Accounting Office to study last week's hearings in an attempt "to determine whether the Maritime Administration and its personnel have violated existing statutes."

Kreps said that the Maritime Administration would continue to promote the maritime industry through its Office of Market Development. She also praised Blackwell, saying "he deserves a great deal of credit for the progress made by the U.S. merchant marine in this decade."