With only a handful of members on the floor, the House yesterday approved a $99 billion increase in the government's debt ceiling to nearly $1.39 trillion. The Reagan administration said the new limit should cover government borrowing needs until the end of September.

The Senate still must act on setting a borrowing ceiling.

House Ways and Means Committee Chairman Daniel Rostenkowski (D-Ill.) said that Treasury borrowing will hit the current $1.29 trillion ceiling by the end of the month.

In earlier years, debate on the debt ceiling often was acrimonious. Conservatives railed against government spending. Because of the difficulty of vetoing such legislation, the debt ceiling increase often was held hostage to other legislative action.

Yesterday, however, the increase was approved by voice vote with a minimum of debate. When House Speaker Thomas P. (Tip) O'Neill declared that the increase had been approved by a voice vote, no one objected to the lack of a quorum, the traditional way to force a roll call vote.

Yesterday, Republicans tried to attach an amendment to the debt-ceiling legislation that would have required a $7 billion cut in spending in fiscal 1983--which ends Sept. 30--but were defeated on an almost straight party-line vote, 249 to 171.

In the debate on increasing the debt ceiling that followed, leaders of both parties urged House members to approve the increase, arguing that enactment of the higher ceiling is a matter of good government, permitting the Treasury to write checks for programs Congress already has approved.

Rep. Jack Kemp (R-N.Y.) said that he used to make approval of a debt ceiling a "fiscal responsibility issue," but conceded yesterday that he was wrong. Rep. Barber Conable (R-N.Y.) said approving an increase is not a "conservative-liberal issue," but one of the administration of government.

The House bill also changed the permanent debt ceiling from $400 billion to $1.39 trillion--all changes in the ceiling since 1971 have been "temporary"--and also authorized the Treasury to issue up to $150 billion in long-term bonds that carry an interest rate higher than 4 1/4 percent. The current bond ceiling is $110 billion.