Bowden said false allegations in news reports compromised his ability "to properly represent" the ball club.
An mlb.com report said Bowden was "under fire for his possible, though denied" connection to the alleged skimming of bonuses of Latin American players. An earlier report, from SI.com, said Bowden was being looked at in a federal investigation into the skimming allegations.
"There have been no charges made, and there has been no indication that parties have found any wrongdoing on my part," Bowden said at the team's spring training site in Viera, Fla. "At the same time, while I have done nothing wrong, I place a greater value on the love, respect, and best interests of my family, friends, the game of baseball ... ."
Bowden said he had "become a distraction" because of "speculation that was swirling."
Jose Rijo, Bowden's special assistant, was fired last week. The team said it would no longer use Rijo's baseball academy in the Dominican Republic. Nationals President Stan Kasten said Rijo was not fired because of the investigation.
Kasten said Bowden "has maintained his innocence but recognized that he had become a distraction, and with great grace determined to do what was best for the team and his players."
Bowden has been with the Nationals since their inception in 2004.