Boston Scientific Corp. yesterday said it has agreed to pay $296 million to settle a US Department of Justice investigation into charges that its Guidant heart-device subsidiary made faulty product reports to the Food and Drug Administration.

The resolution, part of an effort by the company's new top executive to clean up long-running legal issues, more than erased the $200 million profit the company reported for the third quarter.

In a statement, the Natick medical device maker said it recorded a one-time charge against its earnings - equivalent to about 20 percent of its cash on hand - to cover the cost of the settlement. That resulted in a $94 million loss for the three months ending Sept. 30.

The settlement with the Justice department came five weeks after Boston Scientific agreed to pay $716.3 million to rival Johnson & Johnson's Cordis unit to resolve more than a dozen patent lawsuits over heart devices. Industry analysts said the moves suggest Ray Elliott, who took over as Boston Scientific's chief executive in July, is eager to clear away lingering legal problems and move forward with restructuring plans he has alluded to in recent conference calls with investors.

Elliott is "a supremely pragmatic individual,'' said Rick Wise, managing partner at Leerink Swann in New York, an investment bank specializing in health care and life sciences. "He's making the practical decisions to position Boston Scientific for today's global health care environment.

That argues for a more focused company, trying to move past extraneous legal issues that are time wasters and focus on what the company is good at: medical technology and innovation.''

Shares of Boston Scientific edged up 3 cents to $8.08 on the New York Stock Exchange.

But even as it tried to put its legal problems behind it, a new one arose yesterday. Boston Scientific disclosed in a regulatory filing that it received a subpoena from the Office of Inspector General at the Department of Health and Human Services requesting information about contributions made by the company's cardiac rhythm management division - the former Guidant Corp. - to charities with ties to doctors or their families. Such contributions could pose a conflict of interest for a company that sells medical gear to physicians groups and hospitals.

"We are currently working with the government to understand the scope of the subpoena,'' the company wrote in its filing. It declined to provide more details. Don White, a spokesman for the inspector general's office at the health and human services department, confirmed his office issued a subpoena to Boston Scientific on Sept. 26, but said he had no other information about the request.