NEW YORK, DEC. 30 -- Merck & Co., the giant pharmaceutical concern, topped Fortune magazine's latest annual ranking of the most admired U.S. companies for the second year in a row, the magazine said today.

Merck, based in Rahway, N.J., scored the highest overall rating ever in the six years the survey has been conducted. The results appear in the Jan. 18 issue of Fortune, which appears on newsstands Monday.

Second was Rubbermaid Inc., the rubber products company based in Wooster, Ohio. Rubbermaid was rated fifth a year ago.

Third was Dow Jones & Co., the New York-based publisher of The Wall Street Journal and other financial publications, up from ninth a year ago.

International Business Machines Corp., which ranked as the most admired company in each of the first four Fortune surveys, slipped out of the Top 10 listing for the first time.

The computer giant, based in Armonk, N.Y., fell to 32nd place from the eighth spot last year.

At the bottom of the list of 306 companies was Financial Corp. of America, based in Irvine, Calif., and operator of the nation's largest savings and loan. FCA has taken heavy loan-loss provisions in recent years.

On the most-admired list, Procter & Gamble Co., the consumer products giant based in Cincinnati, ranked fourth, up from 18th a year ago, and Liz Claiborne Inc., the clothing maker, finished fifth, down from second a year ago.

Next were Minnesota Mining & Manufacturing Co., the scientific and photographic equipment company based in St. Paul, Minn.; Philip Morris Cos. Inc., the tobacco, food and beverage company based New York; and J.P. Morgan & Co., the New York-based commercial banker.

Tied for ninth place were newcomers to the Top 10 -- RJR Nabisco Inc., the tobacco and foods company based in Winston-Salem, N.C., and Wal-Mart Stores Inc., a retailer based in Bentonville, Ark.

The rankings are based on 3,480 replies to a survey of more than 8,000 top executives, outside directors and financial analysts.

Ninety percent of the returns were in hand before the Oct. 19 stock market plunge.

Those surveyed were asked to rate the 10 largest companies in their own industries on eight key attributes, including quality of management, quality of products or services, innovativeness, long-term investment value, financial soundness, community and environmental responsibility, use of corporate assets and ability to attract and keep talented people.

Ratings were on a scale of zero to 10 with 10 being the best mark, and included 33 industries with assignments being made according to the business that contributed the most to a company's 1986 sales.

Merck ranked first according to each of the eight attributes but one -- community and environmental responsibility in which Johnson & Johnson, a pharmaceutical and medical products company based in New Brunswick, N.J., was ranked first.

Merck expects its 1987 profits will rise 30 percent on a 20 percent sales increase amid strong demand for its cardiovascular drugs and antibiotics. It also rolled out a cholesterol fighter -- Mevacor -- in September.

Second from the list's bottom was American Motors Corp., based in Southfield, Mich. It recently was acquired by rival auto maker Chrysler Corp.

Others in the bottom five, listed in ascending order, were BankAmerica Corp., the commercial banking firm based in San Francisco; LTV Corp., the metals company based in Dallas; and Bethlehem Steel Corp., a metals maker based in Bethlehem, Pa.

Taking the biggest tumble in the rankings was Allegis, the Chicago-based parent of United Air Lines. It fell to 290th place, from 188th a year ago.