The Red Sox admitted to the commissioner's office that their trainers had received signals from video replay personnel and then relayed that information to some players, according to a report in the New York Times on Tuesday.
"I'm not going to comment on what's been written or any of that, but this has been a concern of mine in baseball for a long time," Yankees manager Joe Girardi said. "There has to be a way to protect signs.
"Electronics is the world we live in today. (Things) continue to change as we move on. There has to be something that a catcher and pitcher and middle infielders can do to combat all this.
"Football went to headset. I think we have to try something."
Major League Baseball was alerted to the scheme, which included a trainer in the dugout looking down at his Apple Watch and relaying a signal to players, who may have used the information to determine the type of pitch being thrown, by the Yankees.
"Obviously, every game we play against those guys is a big game and an (important) game, they're probably looking for any little edge that they can get," Yankees outfielder Brett Gardner said.
New York general manager Brian Cashman filed a complaint with the commissioner's office, including video shot of the Boston dugout.
"Aware of the rule. Electronic devices are not to be used in the dugout, but beyond that the only thing I can say it's a league matter at this point," Red Sox manager John Farrell said.
Baseball investigators corroborated the Yankees' claims, according to the New York Times.
The Red Sox responded by filing their own complaint on Tuesday, alleging that New York uses cameras from its television broadcast on the YES network to steal signs.
"No chance. No, we're not doing it," Girardi said of Boston's counterclaim.
No discipline has been announced.