Hedge fund manager Steven A. Cohen, founder and chairman of SAC Capital Advisors. (STEVE MARCUS/REUTERS)

SAC Capital Advisors agreed to pay $616 million to resolve two civil lawsuits involving affiliates accused of insider trading, a massive settlement from the legendary and beleaguered hedge fund run by billionaire Steven A. Cohen.

The Securities and Exchange Commission announced Friday that CR Intrinsic Investors will pay $602 million, a record sum for an insider-trading case. The other affiliate, Sigma Capital Management, settled for nearly $14 million. Neither entity admitted nor denied wrongdoing, and their agreements await court approval.

For years the government has suspected SAC of profiting from illegal trading tips. At least five people have been accused of insider trading while they worked for the hedge fund. Federal authorities have never charged Cohen, but the government’s persistent scrutiny of his firm has sullied his mythical status in the hedge fund world.

The most damaging case was the one involving CR Intrinsic and one of its former portfolio managers, Mathew Martoma, who was charged by the government with running the most lucrative insider-trading scheme ever while working closely with Cohen.

In separate cases, federal prosecutors and the SEC accused Martoma of getting secret tips from a neurologist about the results of a clinical trial involving an Alzheimer’s drug. The tips allegedly enabled the hedge fund and others to make more than $276 million in illegal profits or avoided losses. Martoma denies the charges.

In November, about a week after the government filed its cases against Martoma, SAC revealed that the SEC was preparing to file civil charges against the hedge fund, stirring speculation about whether Cohen would get ensnared. Investors pulled $1.7 billion from the fund, which had about $15 billion of assets under management.

The settlements Friday resolve the civil case that the SEC was contemplating, but speculation about Cohen continues.

“My thinking is he’s not out of the woods,” said Marc Powers, a securities partner at Baker-Hostetler and a former SEC enforcement attorney. “All you need is Martoma to say he revealed to Cohen what [the neurologist] told him, and Cohen would be in hot water.”

The SEC also said as much. George Canellos, acting director of the SEC’s enforcement division, told reporters that the settlements do not preclude any future charges against other people or entities, including Cohen. “We cannot tolerate a market rigged for the benefit of insiders and their cronies,” Canellos said.

Martoma continues to fight the civil and criminal charges pending against him.

“SAC’s business decision to settle with the SEC in no way changes the fact that Mathew Martoma is an innocent man,” said Charles Stillman, the lawyer representing Martoma. ”We will never give up the fight for his vindication.”

The settlement involving CR Intrinsic ranks as one of the largest ever assessed in an SEC action and exceeds the $400 million paid by Michael Milken to settle civil charges in 1990, including insider trading and stock ma­nipu­la­tion.

The SEC’s lawsuit against Sigma Capital was filed Friday in federal court in Manhattan, along with the settlement. In that case, the government accused Sigma Capital of using non-public information obtained by one of its analysts, Jon Horvath, about the earnings of Dell and Nvidia.

Horvath, who pleaded guilty earlier this month, learned about the companies’ 2008 and 2009 earnings in advance, and Sigma Capital traded on the confidential information for $6.4 million in gains, the government said.

The investigation began last year with charges against Horvath and several other analysts and hedge fund managers.

The money to cover the settlements will come from SAC’s management company, meaning investors won’t pay the costs.

Jonathan Gasthalter, a spokesman for SAC, said the firm is happy to have both settlements behind it.

“This settlement is a substantial step toward resolving all outstanding regulatory matters and allows the firm to move forward with confidence,” Gasthalter said in a statement. “We are committed to continuing to maintain a first-rate compliance effort woven into the fabric of the firm.”