Allegations of retaliation, race and sex discrimination were the top three reasons why employees last year filed discrimination complaints against their employers.

The Equal Employment Opportunity Commission reported this week that it received a total of 99,412 discrimination filings by workers in fiscal 2012.

Thirty-eight percent of those bias charges, the highest percentage, dealt with retaliation. Those claims alleged that employers took negative action against employees for such things as whistleblowing or exercising other rights.

Nearly 34 percent of the bias claims dealt with race-based complaints, and 30.5 percent with sex. The sex discrimination category includes harassment — both opposite sex and same sex — and pregnancy discrimination.

Smaller numbers of complaints were filed by workers alleging discrimination regarding disability ( 26.5 percent); age (23 percent); national origin (11 percent); religion (nearly 4 percent). and color (nearly 3 percent).

The federal agency said it recovered $365.4 million from private, state and local government employers in connection with cases won by employees.

In the EEOC’s fiscal year, which ended Sept. 30, the agency itself filed 122 lawsuits in behalf of workers when its investigators found patterns of discrimination or particular examples that the agency wanted to pursue.

Also, the agency’s legal staff resolved 254 lawsuits for monetary recovery of $44.2 million. And, without litigation, the agency said it obtained settlements or conciliation agreements that produced $36.2 million for employee victims of discrimination.

The agency, which had been dealing with a backlog of cases, said that it has made headway in the last two years by reducing the pending case inventory by 10 percent a year.