The treasury department yesterday disclosed that at least 5,200 ounces of the nation's gold - and possibly much more - has mysteriously vanished, some of it likely going up in smoke and some of it perhaps stolen by sticky-fingered employes.

The loss, valued at more than $1.1 million, was discovered at the New York Assay Office, the sole government facility for melting and refining gold into finished bars. Officilas said the office and its 85 employes have been under intense investigation for several months regarding allegations of wide-spread irregularities.

Sen. William Proxmier (D-Wis). chairman of the senate banking committee and the one who initially asked for an investigation, yesterday called the disapperance "the ultimate golden fleece."

It is the largest disapperance of government owned gold from a federal facility in the nation's history, and only the second such case on record. The first occured in 1955, when 1,800 ounces of gold were reported missing from a Denvermint. That loss was susequently blamed on an elderly employe who gave the gold away.

Government investigators say they still are not sure whathappened to the missing gold this time. "Several investigations are still goin on," Joseph Laitin, a tresury spokesman, told reporters. "We don't have anything conclusive yet."

Laitin suggested that some of the gold may simply "have gone up the chimney," floating up with smoke particles as part of the normal melting process. He quoted gold experts as allowing for a loss of up to 1,000 parts of gold for every 1 million parts refined. More than half of the loss, Laitin said, might be explained this way.

But he added that the possiblity of theft had not been eliminated.

According to congressional sources, government investigators claim that in at least some cases gold was taken out ot the assay office by employes who wrapped the metal in newspaper and then held it in their fingertips with their arms outstretched while security guards at the door searched the rest of their bodies with metal detectors.

The investigation has been complicated by what Treasury officials describe as very antiquated accounting and management methods used by the New York office - some of which reportedly date back to the establishement of the office 1854.

The losses reported so far are the result of a Treasury audit of the period 1973-77. Officials indicated that further audits may uncover other significant amounts of unaccounted for back to 1854," Laitin said.

In a letter sent to Proxmire yesterday, Robert Carswell, deputy secretary of the treasury, worte, "The full truth may never be known, because of the inadequate records kept over the years."

Much of the gold in the assa office was sold to the government by the public in the form of gold nuggets, jewelry and coins until 1969, when the government stopped purchasting gold. The office is responsible for refining the gold into bars for storage.

In addition, the office, at 32 Old Slip St. in Manhattan's Wall Street district, also serves as a gold storage center. About 55 million ounces of gold, or more thatn one-fifth of the nation's total reserves, are stored there.

The Treasury Department first investigated the office a year ago at Proxmire's request after he received a letter from what appeared to be a former employe of the office alleging serious irregularities. But the employe later claimed that the letter was a forgery, and Treasury dropped the probe.

However, the department decided to reopen the investigation three months ago after an office employe was caught trying to walk out with several small gold pieces.

"A subsequent and more thorough investigation has revealed there were no systematic security procedures at the New York office," Proxmire said in a statement yesterday, "and that employes may have been walking out with hudnreds of thousands of dollars in U.S. gold that belongs to the U.S. taxpayer."

Treasury officials said they have taken steps to guard against fruther losses and irregularites at the New York facility. Security procedures have been tightened and several changes in management have been institued, they said.