During an appearance on MMAfighting.com's "MMA Hour" Monday, Overeem revealed the promotion asked him to compete on the specific date and threatened to cut him from the tournament if he didn't agree.
In an email to ESPN.com, Overeem's manager Bas Boon said he regretted some of Overeem's statements and added the two sides were still negotiating.
"The management is still in negotiations with the UFC/Strikeforce," Boon wrote. "We regret that Alistair said certain things in this interview. However, we do understand that Alistair is getting frustrated about the whole situation."
According to a source familiar with Overeem's deal, Alistair has one fight remaining on his deal after beating Werdum.
Strikeforce officials have confirmed to ESPN.com that although Overeem has been taken out of the tournament, he remains under contract with the promotion.
Overeem (35-11), who advanced to the semifinal stage with a unanimous decision win over Fabricio Werdum in June, fought through the injured toe in his last performance but wouldn't risk doing so again.
The Strikeforce heavyweight champion is unbeaten since September 2007 and was considered a favorite to win the Grand Prix.
"When Alistair fought Werdum he broke his toe in training," said Boon. "He wanted to make sure to be 100 percent for his upcoming fight against (Silva).
"Therefore, we have a difficult situation, which causes pressure on both sides. We really would like to work things out for this tournament and will do our best in finding a solution acceptable for all involved parties."
Undefeated heavyweight prospect and former U.S. Olympic wrestler Daniel Cormier has been tabbed to take Overeem's place in the tournament.
Reached via text, Cormier's trainer, Javier Mendez, said "yes" his fighter will replace Overeem and fight Silva.
When contacted by ESPN.com earlier Monday about Overeem's replacement, Strikeforce officials responded nothing was official yet.
Brett Okamoto covers mixed martial arts for ESPN.com. MMA writer Josh Gross contributed to this report.