The Jays issued a statement Tuesday that said employees won't be permitted to leave for the same job in another organization — essentially blocking a move by Farrell back to the Red Sox.
"Due to the distraction caused by media speculation regarding our employee permission policy, the Toronto Blue Jays have amended their policy and will not grant permission for lateral moves," the team said in a statement.
General manager Alex Anthopoulos had previously said employees were permitted to speak with any team about any job.
During a conference call on Tuesday, he was reversed course.
"Totally, 100 percent, lateral moves (will be blocked)," Anthopoulos said. "That's exactly the way it reads."
Farrell spent four seasons as Boston's pitching coach before being hired to manage the Blue Jays last year. The team finished fourth in the AL East with an 81-81 record in his first season on the job.
On Sunday, the Boston Globe reported the Red Sox had interest in bringing Farrell back as manager.
Anthopoulos said the speculation about Farrell was becoming a distraction.
"I think we have to constantly adjust to the times," Anthopoulos said. "The game continues to change and we have to continue to adjust to make sure that we maintain the core values of the ball club."
The Red Sox are going through a shakeup following one of the biggest September collapses in major league history. They blew a nine-game lead in the wild card over the final month of the season and missed the playoffs.