NEW YORK, DEC. 27 -- An early-morning transformer explosion and fire in lower Manhattan delayed stock trading nationwide for 90 minutes today, the third time this year that markets have been closed because of power failures.

The fire at the 55 Water St. skyscraper in southern Manhattan broke out shortly after midnight, sending smoke into the offices of Securities Industry Automation Corp. (SIAC), a joint venture between the New York and American stock exchanges that controls the computer system through which most trading is transacted and recorded.

New York Stock Exchange spokeswoman Sharon Gamsin said that in the next 12 to 14 months SIAC will have a backup facility across the East River in Brooklyn.

The New York and American exchanges were the first to announce that the usual 9:30 a.m. opening would be delayed.

But the nation's regional stock exchanges also refrained from trading, bowing to a request from the Securities and Exchange Commission.

SEC spokeswoman Mary McCue said the regulatory authority wanted all the markets to reopen at the same time to give all investors an equal opportunity to buy or sell stock.

As the business day dawned on Wall Street, hundreds of workers milled about the chilly streets while others followed instructions on handwritten notes by the doors of the Water Street building and reported for work elsewhere.

Citibank, the nation's biggest banking company, which occupies several floors of the building, relocated employees to other offices in the city.

Despite the upheaval in the streets, market observers said the fire did not cause too much of a problem for investors.

Stock trading was thin and largely directionless because of the holidays, with the Dow Jones industrial average ending the day down nearly 12 points.

Twice before during the year, trading was halted by power problems. On Aug. 13, a fire at a Con Edison power substation forced the American Stock Exchange, New York Mercantile Exchange and other futures markets in southern Manhattan to close by early afternoon, but the New York Stock Exchange was not affected. And on Nov. 23, a power failure delayed trading on the NYSE for 90 minutes shortly after the opening bell.

Though the fire that caused today's problem was under control by 3:16 a.m., officials feared hazardous polychlorinated biphenyls, or PCBs, may have contaminated several floors of the 54-floor skyscraper.

Samples of materials from the building were taken to an Environmental Protection Agency lab for analysis, but the building later was found to be untainted by the cancer-causing substance.

Once trading opened at about 11 a.m., stocks began a slow downward drift, despite continued strength in the bond market, where the 30-year Treasury bond ended the day up 15/32.

At the close, the Dow stood at 2625.50, down 11.63. Declines outpaced advances on the Big Board by a ratio of about 3 to 2 on light volume of 102 million shares.

Among industry groups, bank stocks were down slightly by midday but the decline steepened in the afternoon. Four money-center banks posted losses of more than a point: Morgan dropped 2 to 44 by the close, Bankers Trust sank 2 1/8 to 42 1/8, Bank of New York lost 1 to 17 7/8 and First Chicago gave up 1 1/4 to 16 1/2.

Tiffany and Co., for example, finished down 2 1/4 at 35, extending a 4 3/8 loss on Wednesday that followed late-1990 sales estimates implying imminent downgrades of next quarter's earnings projections.

On the American Stock Exchange, electronic-systems manufacturer Cubic Corp. closed down 2 1/4 points at 15 3/4 for a 12.5 percent decline on the day. The company reported lower quarterly earnings due to settlement provisions for a longstanding Justice Department investigation into the company's Cubic Defense Systems unit.

The Dow transports eased 8.81 to close at 913.42, while the interest-rate-sensitive utilities slipped 0.88 to 210.45 despite a nearly half-point gain in U.S. bonds as stocks closed.

Among broad stock indexes, the Standard & Poor's 500 was down 2.56 at 328.29, the NYSE Composite down 1.12 to 179.48, the Value Line down 1.01 at 239.40, the Amex Market Value down 1.32 at 303.67 and the Nasdaq Composite down 1.34 at 371.06.