The D.C. Council approved an emergency measure yesterday to allow this year's pay increases for more than 12,000 nonunion city employees to be retroactive to Oct. 1, the beginning of the current fiscal year.

The council's action immediately gives the 300 supervisory officials in the police department retroactive 3 percent pay raises at a cost of $1 million, according to city officials. The 3,600 unionized rank-and-file officers already have received retroactive 3 percent pay increases negotiated in December and approved by the council.

Meanwhile, pay proposals for the city's remaining nonunion supervisors -- including council members and their aides -- and 20,000 union employees are expected to come before the council within 90 days. City officials estimate that pay increases for nonunion employees will total $13 million in 1988.

Council Chairman David A. Clarke said the emergency legislation, which was requested by Mayor Marion Barry, was needed to clear up confusion in the current law about the retroactive date for the 1988 pay raises.

Council member Betty Ann Kane (D-At Large), who voted against the emergency measure, said, however, that the council should complete the budget review process and determine what the city can afford before deciding the retroactive date.

"We decided -- without seeing the numbers, without seeing what the union people are going to get -- that the bosses would get a pay raise retroactive to Oct. 1," Kane said after yesterday's session.

But other council members argued that to delay action would create inconsistency in pay for union and nonunion employees. Council member Wilhelmina J. Rolark (D-Ward 8), who heads the council's Judiciary Committee, which oversees the police department, urged her colleagues to support the measure "in the interest of fairness."

Although the police department is the only city agency yet to have its pay proposals approved by the mayor and the council, city officials said yesterday that most of the unions representing city employees, except for the firefighters, have voted to ratify their negotiated pay proposals or are preparing to vote on them.

The mayor has generally submitted pay proposals for nonunion employees after the labor organizations representing union employees have agreed to negotiated contracts.