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. Officials said the office and its 85 employes have been under intense investigation for several months regarding allegations of widespread irregularities.

Sen. William Proxmire (D-Wis.). chairman of the Senate Banking Committee and the one who initially asked for an investigation, yesterday called the disappearance "the ultimate golden fleece."

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

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

Latin 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 possibility of theft has not been eliminated.

According to congressional sources, government investigators claim that in at least some cases gold was taken out of 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 establishment of the office in 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 gold. "For all we know, the losses go back to 1854," Laitin said.

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

Much of the gold in the assay office was sold to the government by the public in the form of gold nuggets, jewelry and coins until 1969, when the government stopped purchasing 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 than 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 hundreds 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 further losses and irregularities at the New York facility. Security procedures have been tightened and several changes in management have been instituted, they said.