Baltimore and the District of Columbia trimmed their government work forces by larger percentages than any other big cities in the country between October 1980 and October 1981, the Census Bureau reported yesterday.

Baltimore led the nation, according to the study, by cutting its work force from 44,191 to 37,563, a 15 percent drop. The District was second, cutting the size of its staff by 10.6 percent, from 45,473 to 40,642.

The cuts came as officials in both cities struggled to balance their budgets in the face of dwindling federal aid.

About 2,700 of the workers cut in Baltimore were employed under the Comprehensive Employment and Training Act (CETA), a public service employment and job-training program that the Reagan administration largely abolished a year ago. Baltimore laid off 1,000 other employes, and most of the rest left the city work force and were not replaced, city officials said.

In Washington, city personnel official Robert Storey said most of the cuts were made through attrition, although city agencies under Mayor Marion Barry's control laid off 148 workers in the year ending last October, compared with 367 the year before.

He said there were no layoffs in the fiscal year that ended Sept. 30, although the size of the city work force declined again, to a current figure of 39,446. Storey said the reduction of 1,196 in the last year was attained almost entirely through attrition.

Baltimore's work force now totals about 37,300, according to Edward Seidler, the city's deputy personnel director. "As vacancies occur," he said, "we're not filling them."

Nationwide, city governments employed 2,469,000 workers in October 1981 and had payrolls totaling $3.2 billion in that month, according to the census report. That is a 3.6 percent reduction in the size of the city work forces over October 1980, but a 9.5 percent increase in the payroll costs. The period marked the fourth year in the past six that the Census Bureau has found a decline in the number of full-time city government workers.