Farrell had been mentioned in a recent article by the Boston Globe as a potential candidate to replace former Red Sox manager Terry Francona.
The 49-year-old Farrell addressed that speculation for the first time on Monday morning in what appeared to be an attempt to put an end to the rumor.
"I have no idea and no comment on what's happening in Boston," Farrell wrote to sportsnet.ca. "I am focused right now on preparing for what is best for the Blue Jays in 2012."
Jose Bautista, in Arlington to receive his second Hank Aaron Award, asserted that he and his teammates want Farrell to remain in Toronto.
"Hopefully he'll stay on board with us," Bautista said. "We went through a period of transition from Cito [Gaston] to [Farrell], and now we feel comfortable with him. And I feel he did a great job managing our team, given all the difficulties of our season with injuries, trades, roster shuffles [and] some guys maybe not performing up to their capabilities. And we still finished at .500.
"I think he knows we want him to stay. I don't think we need to pitch ourselves to him. When it comes down to it, he's going to have to make a decision based on his career, his family and where he feels comfortable. Unfortunately, if that means him going to the Red Sox, we're just going to have to find a new manager. But I'm hopeful that doesn't happen."
Farrell spent four seasons as the pitching coach in Boston from 2007-10. He had long been considered the heir apparent to Francona but opted to make the transition to Toronto in October of 2010.
The New Jersey native led the Blue Jays to an 81-81 record during his first year as a manager. Farrell developed a strong working relationship with general manager Alex Anthopoulos and it appears doubtful he would consider jumping ship after just one year.
Per club policy, Toronto did not release the terms of Farrell's contract, but it is believed the former pitcher is locked up for the next two seasons. Boston would need to ask for the Blue Jays' permission to speak to Farrell and that had not occurred as of Sunday night.
Assistant general manager Tony LaCava is also potentially being recruited by one of Toronto's American League East rivals. LaCava had an interview last week in Baltimore for the club's open general manager position.