Federal prosecutors yesterday lost one opportunity to build a case against hedge fund manager Steven A. Cohen when a grand jury indicted one of Cohen’s former employees on charges related to an insider trading scheme, severely reducing the possibility he would cooperate as a witness against Cohen.

The grand jury returned an indictment against Mathew Martoma, a former portfolio manager at CR Intrinsic Investors, one of SAC Capital Management’s funds, in what prosecutors have called the “most lucrative” insider trading scheme ever.

Martoma, 38, of Boca Raton, Fla., was indicted on three counts of conspiracy to commit securities fraud and securities fraud related to trades made in Elan Corp. and Wyeth based on tips prosecutors say he received from a doctor. The trades allegedly helped CR Intrinsic avoid losses and reap profits totaling $276 million in the summer of 2008. The indictment followed an earlier criminal complaint filed Nov. 20.