Washington Nationals general manager Jim Bowden responded Monday to a report that he’s part of a federal investigation into the skimming of signing bonuses given to prospects from Latin America, saying he’s done nothing improper.

‘‘I’m innocent of any wrongdoing,’’ Bowden said. ‘‘Aside from that, no comment.’’

Citing an unidentified baseball executive familiar with the investigation, SI.com reported Sunday night that the FBI is looking at Bowden’s actions as far back as 1994, when he was GM of the Cincinnati Reds.

Bowden met last year with FBI investigators looking into an alleged scam involving skimming signing bonuses for players from the Dominican Republic.

Nationals president Stan Kasten made it clear that this is a separate issue from that of Esmailyn Gonzalez, the Washington player who earlier this week was found to have lied about his age and name. Gonzalez received a $1.4 million signing bonus in 2006 when the Nationals signed what they thought was a 16-year-old shortstop.

‘‘That is a different thing than the whole Esmailyn Gonzalez stuff,’’ Kasten said. ‘‘Esmailyn Gonzalez is a piece-of-discrete thing that involved just us. This is obviously something much wider ranging.’’

Last year, the Chicago White Sox fired director of player personnel David Wilder and two other scouts in the club’s Latin American operation after a two-month investigation by Major League Baseball’s Department of Investigations.