A Senate Governmental Affairs subcommittee, despite warnings of a presidential veto, has approved a bill to strengthen the independent-counsel law and make it permanent.

The nine-member subcommittee was polled by letter last week after the Justice Department attacked the system of appointing independent counsels to investigate criminal allegations against top government officials.

According to an incomplete tally, the members endorsed the legislation 6 to 1. Sen. Ted Stevens (R-Alaska) voted against the reauthorization bill, and Sen. Warren B. Rudman (R-N.H.) abstained. The vote of Sen. Jeff Bingaman (D-N.M.) had not been recorded.

The Justice Department last week called the law unconstitutional and charged that the system was riddled with inordinate expenses, excessive delays and trivial investigations. Assistant Attorney General John R. Bolton said that if the Senate bill is enacted, "we will have no choice but to recommend its disapproval by the president."

White House officials winced at some of Bolton's language but confirmed that his assessment represented the administration's position.

Six independent counsels, including two whose assignments are under seal, are investigating present and former high-ranking Reagan administration officials, including Attorney General Edwin Meese III.

The independent counsel statute was first enacted in 1978 and revised and reauthorized in 1983 on President Reagan's signature. It will expire in January unless Congress renews it.

Aides to Sen. Carl Levin (D-Mich.), the reauthorization bill's main sponsor, said he will seek a mark-up by the full committee in early July and hopes to win Senate passage before the August recess. Similar legislation is pending in the House, where its chief sponsor, House Judiciary Committee Chairman Peter W. Rodino Jr. (D-N.J.), has predicted passage.

The bill approved by the Senate subcommittee includes a provision to protect an independent counsel from being removed for refusing to obey a presidential order if the order "would compromise the independence" of the investigation.

The Justice Department argues that the president would have the right, even under the 1978 law, to fire an independent counsel who disobeyed a "lawful direction of the president."

Another provision, the only major change since the bill's introduction last month, would open records of past independent-counsel investigations under the Freedom of Information Act. The National Archives and Records Administration would process FOIA requests for such records, which are now kept under seal by the three-judge federal panel that appoints independent counsels and receives their reports.

Levin and the bill's chief cosponsor, Sen. William S. Cohen (R-Maine), have described it as an effort to insulate the law from what they describe as the administration's "guerrilla warfare," including missed deadlines, prolonged "threshold inquiries" before an independent counsel is appointed and Meese's failure "to recuse himself from cases that he should have."

Meese is under investigation partly for failing until April to disqualify himself from all federal investigations of Wedtech Corp., a defense contractor, although he intervened on the company's behalf in 1982 as a White House official and later engaged a Wedtech consultant to handle his investments.