Red Sox general manager Theo Epstein said that "there's no disconnect" in response to questions regarding his relationship with manager Terry Francona, according to Boston.com's Extra Bases blog.
Veteran baseball analyst Peter Gammons raised the concern on Thursday on a national radio show.
"I've sensed an increasing disconnect between Theo Epstein and Terry Francona," he said.
Epstein refuted the allegations in an email Friday.
"There's no disconnect," he wrote. "We've had each other's support and admiration for eight years and that doesn't change because the team has had a very difficult month so far."
The Sox currently hold a two-game lead in the AL wild card race. They begin a three-game series in New York against the Yankees Friday.