Congress voted yesterday to keep the federal cigarette tax at 16 cents a pack through Nov. 14 as part of an omnibus bill to extend a half-dozen programs scheduled to expire as the 1985 fiscal year ended last night. President Reagan signed the cigarette tax measure, despite reports that he might veto it.

In a separate bill, Congress approved a 45-day extension of dairy price supports and related farm programs that also had been due to lapse last night. Reagan is expected to sign the legislation, although the White House said he had not received it last night.

Administration officials had said yesterday there was a "distinct possibility" that Reagan would veto the bill containing the cigarette tax extension. But the White House announced early today that the president had signed the bill before midnight. A spokesman provided no explanation on the president's decision to approve the cigarette tax extension.

Without the president's signature, the cigarette tax would have dropped back to its pre-1982 level of 8 cents at midnight.

In the past, administration officials have said that Reagan, who generally advocates lower taxes, thinks that the cigarette tax is the kind of tax that should be left to the states.

Both the House Ways and Means Committee and Senate Finance Committee have proposed permanent extensions of the 16-cent levy in deficit-reduction legislation that is scheduled for floor action in both chambers in the next week or two. The federal government would lose an estimated $6 million for each day the cigarette tax is not in effect.

Other programs wrapped into the cigarette tax bill included trade adjustment assistance for firms and workers hurt by import competition, rates for reimbursement of doctors and hospitals under Medicare and borrowing for the railroad retirement program.

Passage of the stopgap measures was required because Congress, running behind schedule on most major legislation, has not yet passed permanent reauthorization of the programs, which in some cases are expected to include far-reaching overhauls.

It was required to "protect individuals . . . from bearing the cost of Congress' delay," said House Ways and Means Committee Chairman Dan Rostenkowski (D-Ill.).

But the rush to usher in the new fiscal year, which started today, came without the contentious delays that normally accompany stopgap financing for the government as a whole. A "continuing resolution" to finance government agencies for the first 45 days of fiscal 1986 passed easily last week.

Reagan signed the funding measure yesterday and, in a statement, said spending bills should be "consistent with both the need for restraint in domestic spending and support of the defense and international interests of the nation.

"As we meet with the Soviets to discuss sensitive and important arms-control issues, it is particularly important that we not be hindered by lack of congressional action on, or inadequate support for, our fiscal '86 national security programs," he said.

Lawmakers are expected to square off over issues ranging from budget deficits to foreign policy in connection with debt-ceiling extension legislation, expected to come to the Senate floor this week.

The extensions passed yesterday originally were supposed to cover the Superfund toxic-waste cleanup program as well, because authority for it also expired last night. Congressional aides said disputes between committees forced the House leadership to delay the Superfund extension until today.