By Jonathan Stempel and Jennifer Saba

NEW YORK (Reuters) - A federal judge threw out a lawsuit accusing Bloomberg LP of discriminating against dozens of pregnant employees, saying the Equal Employment Opportunity Commission's mishandling of the case effectively cost the plaintiffs their day in court.

Monday's decision in the six-year-old case, by Chief Judge Loretta Preska of the U.S. district court in Manhattan, is the latest win for the financial news and information company, whose majority owner is New York City Mayor Michael Bloomberg.

In August 2011, Preska said the EEOC, which enforces federal laws against workplace discrimination, could not pursue a class action. She said there was a lack of evidence that discrimination was Bloomberg's standard operating practice, even if there were "several isolated instances" of individual bias.

Preska on Monday said the EEOC caused unfair prejudice to Bloomberg by failing to properly investigate the bias claims of 29 individual plaintiffs it represented, and by spurning the company's attempts to settle.

She said this "blatantly" contravened the emphasis under Title VII of the Civil Rights Act of 1964, a federal workplace bias law, on settling disputes rather than litigating, justifying the lawsuit's dismissal.

"The court does not impose this severe sanction lightly and recognizes that certain ... claims may be meritorious but now will never see the inside of a courtroom," Preska wrote.

An EEOC spokeswoman said: "We are considering our options and reviewing the court's opinion."

Bloomberg LP spokesman Ty Trippet had no immediate comment.

Michael Bloomberg is not a defendant in the case and has not had an active role at the company since becoming mayor nearly 12 years ago. Bloomberg LP employs more than 15,000 people.

The EEOC originally sued in September 2007, accusing Bloomberg of "pervasive bias" against several dozen women who were pregnant or had returned from maternity leave.

This bias allegedly led to reduced pay and responsibilities, demotions, exclusion from management meetings, and the subjecting of women to stereotypes about female caregivers, the EEOC said.

Preska on Monday said letting the case continue "would severely undermine if not completely eviscerate" Title VII's enforcement procedures, expand EEOC power far beyond what Congress intended, and "greatly increase" litigation costs.

She said Congress "surely did not intend that employers, even ones whose workplaces might be rife with sex discrimination, face the moving target of allegedly aggrieved persons that Bloomberg faced."

In a separate, 181-page decision, Preska dismissed pregnancy bias claims brought by five individual plaintiffs, while allowing part of a case by a sixth plaintiff to go forward.

Bloomberg competes with Thomson Reuters Corp (TRI.TO).

The case is EEOC v. Bloomberg LP, U.S. District Court, Southern District of New York, No. 07-08383.

(Reporting by Jonathan Stempel and Jennifer Saba; Editing by Eddie Evans and Steve Orlofsky)