The House and Senate reaffirmed support yesterday for conflicting versions of balanced-budget legislation as one of its strongest advocates in the White House, chief of staff Donald T. Regan, privately questioned whether it would have a more severe impact on defense spending than previously estimated, according to administration sources.

Officials said that Regan, who was instrumental in persuading President Reagan to endorse the legislation, took a sharply skeptical approach in a White House senior staff meeting yesterday. Regan indicated to other aides that he feared the legislation would make it impossible for the president to get the defense-spending compromise agreed to earlier this year with Congress.

Regan was "very unhappy" in his questioning about modifications to the Gramm-Rudman-Hollings legislation, the sources said, and suggested that changes made since Reagan endorsed it may force the president to reject it. "We've been bled down," said one official who was present, "and we may be fully justified to say, 'Let the thing go.' "

The chief of staff's questioning was important because, until now, he and his subordinates have insisted that Reagan would not have to compromise his defense-spending goals. Previously, Regan had dismissed as unwarranted criticism of the legislation from Defense Secretary Caspar W. Weinberger and others in the administration.

The congressional action yesterday, on legislation to force a balanced budget by 1990 or 1991, set the stage for renewed negotiations to achieve a compromise in the next 10 days.

The issue goes to a House-Senate conference committee, which may convene as early as today in hopes of resolving the dispute before the Nov. 14 or 15 deadline for passage of provisions raising the debt ceiling to $2 trillion.

Senate Finance Committee Chairman Bob Packwood (R-Ore.), chairman of a conference that broke up a week ago in deadlock over the issue, suggested separate negotiations involving House Speaker Thomas P. (Tip) O'Neill Jr. (D-Mass.), Senate Majority Leader Robert J. Dole (R-Kan.) and the White House.

"This is a political judgment that has to be rendered by people who are in a position to enforce a political decision," Packwood said. Senate Budget Committee Chairman Pete V. Domenici (R-N.M.) agreed, contending that the dispute "ultimately will be resolved by the leadership."

The congressional steps toward resumption of negotiations came as the president renewed criticism of the House plan and called for a compromise that would protect his military buildup.

In action yesterday, the Senate voted 74 to 24 for a modified version of the plan it approved last month by roughly the same margin to reduce deficits from $180 billion to zero by fiscal 1991.

The House voted 248 to 177 to reject for a second time the Senate alternative and stand by its counterproposal of last week, which would achieve a balanced budget by fiscal 1990 by speeding up the process to include bigger spending cuts this year. The House plan would also make heavier cuts from defense, exempt some programs for the poor from cutbacks and lift the restrictions during a recession.

Among modifications approved by the Senate were provisions excluding federal pay from cutback requirements, some relaxation of the requirements during economic slowdowns and a slight tightening of the trigger for spending cutbacks this year. The Senate did not consider the House plan.

The Senate wants a first-year ceiling of $180 billion; the House wants a target of $161 billion.

The balanced-budget measure has been tied to the $2 trillion debt-limit proposal, meaning a budget agreement must be worked out before the ceiling can be raised.