Internal Revenue Service Commissioner Roscoe L. Egger Jr. confirmed yesterday that an IRS employe destroyed between 5,000 and 6,000 pieces of taxpayer correspondence at the service's Austin, Tex., center.

The worker was ordered by a supervisor to get rid of the correspondence, all of it from business taxpayers, according to Robert M. Tobias, president of the National Treasury Employees Union, who provided more detail. The supervisor had portrayed the document destruction as a normal file-cleaning operation, he said. But the employe became suspicious after carrying out the order and reported the act to the center's managers and to the local union president, according to Tobias. The supervisor has since resigned, and Egger said "appropriate action" will be taken.

Egger said the incident took place late last year; union officials said it occurred in January. No tax returns were lost, and Egger said he does not know of any other similar incidents. But he said officials at the other nine regional centers are investigating the possibility of more destruction of documents.

Separately, an official of the General Accounting Office yesterday provided the first confirmation of actual return-tampering in the service's Philadelphia center.

David Attianese, group director of the GAO's general government division, said IRS internal reports confirmed that between 50 and 100 tax returns were found hidden in a women's restroom at the Philadelphia center. No other details of the incident were available.

IRS spokeswoman Ellen Murphy said the service could not confirm Attianese's statement, but several GAO officials said they had seen the written IRS account of the incident.

Anonymous phone calls to the offices of Pennsylvania legislators and accounts carried in press reports have alleged the shredding of a total of 27,000 tax returns, as well as the disappearance and hiding of other returns, at the troubled Philadelphia center. That center, where returns from the District and Maryland are sent, is also behind in processing returns, sending refunds and answering letters.

The IRS has said it has no evidence of return-shredding, but a GAO report released yesterday and reported in yesterday's editions of the Post described several other breakdowns at the center that had resulted in incorrect delinquency notices to as many as 150,000 taxpayers.

The disclosures came at a hearing of the House Ways and Means Committee's oversight panel, which was looking into the adequacy of the IRS' fiscal 1986 budget proposal.

Subcommittee members repeatedly berated Egger for asking for decreases of $30.4 million in spending to $3.5 billion and of 1,254 in staff positions to 86,500. The IRS is struggling with a balky new computer, running way behind in processing returns, facing a large correspondence backlog and seeing its audit coverage decline. Yet officials acknowledge that more employes mean more federal revenue in a time of high deficits.

"You seem like you're straining to find an answer," subcommittee chairman J. J. (Jake) Pickle (D-Tex.) told Egger. "The deficit is growing, tax compliance is getting less, we've got snafus all over the country and you're telling me you need less people?"

Egger stood by his budget, which was pared significantly from his original request to the Treasury Department and then again when it was presented to the Office of Management and Budget