The threatened furlough of about 19,000 employes at the Internal Revenue Service was temporarily averted late yesterday after the agency, caught in a budget veto battle between Congress and President Reagan, was given congressional authority to transfer funds to meet its payroll.

The funds transfer means the IRS employes can report to work today and the rest of the week. But they and thousands of other federal workers still face involuntary layoffs beginning one week from today unless the president and Congress can resolve an election-year budget dispute set in motion by Reagan's Aug. 28 veto of a $14.1 billion supplemental appropriations bill.

Treasury Secretary Donald T. Regan was given the final go-ahead to shuffle agency funds in a hurried telephone call from Sen. James Abdnor (R-S.D.), who chairs the Senate Appropriations subcommittee that oversees IRS funding.

Abdnor had been blocking the funds transfer all day, even though Rep. Edward R. Roybal (D-Calif.), his House counterpart, had approved the move earlier in the day. Approval of both chairmen was required.

The IRS employes involved in the dispute represent nearly one-fifth of the agency's work force, and their duties include collecting delinquent taxes and investigating criminal tax cases.

Pending the funds transfer, the employes had been told they would have to stay off the job until Congress either overrode Reagan's veto or reached a compromise with the president on a new supplemental appropriations bill.

Congress reconvenes today, and the House is scheduled to try overriding the veto tomorrow morning. If the veto is sustained, and congressional sources say the vote will likely be close, a new bill must be passed for Reagan's approval. The delay still could cause furloughs throughout the government by the middle of next week.

Abdnor, who had argued against the veto, said through a spokesman earlier in the day that he opposed the transfer of funds because the IRS had hired 2,000 additional employes during the summer and because the Treasury Department had supported the veto, then turned to the transfer as a means of averting a crisis.

Treasury spokesman Marlin Fitzwater said that the IRS had just begun to hire about 1,200 new collections and examination employes, as authorized by Congress, and that the new hires had no impact on the agency's current shortage of funds.

Instead, Fitzwater claimed, Abdnor was holding up the IRS funds transfer to force Treasury to abandon its plan for consolidating the department's inspectors general, particularly in regard to the operations of the Bureau of Alcohol, Tobacco and Firearms.

Later, in announcing that Abdnor had finally agreed to authorize a shift of $24.3 million, Fitzwater said Regan had agreed "to have further discussions" on the oversight responsibilities of the inspectors general.

But while Regan, who was here, Abdnor in South Dakota and Senate Appropriations Committee Chairman Mark O. Hatfield in Oregon conferred on the situation by telephone throughout the day, the budget impasse and impending payless furloughs caused the most concern among those immediately affected.

The National Treasury Employes Union denounced the president's veto and said any IRS furloughs would be akin to sending the lifeguards home "while the country is drowning in red ink."

Most IRS workers on the East Coast had left for home by the time the temporary funding solution was reached, and a Treasury official said the agency plans to send out mailgrams and set up conference calls to let the employes know they are expected at work today.