The Mets said a search is under way for a new GM, who will work with the team to hire a new manager.
Manuel is the seventh manager this season to lose his job. The final guaranteed year of Manuel's contract expired, and the Mets declined to exercise the club's option on the deal.
The Mets were 79-83 this year, a disappointing 18 games behind Philadelphia in the NL East despite having an opening-day payroll of $133 million that was the fifth-highest in the majors. They have not been to the playoffs since coming within a game of going to the World Series in 2006.
"Changes like these are never easy, especially when you are dealing with people you like and respect," Wilpon said.
Manuel was promoted from bench coach on an interim basis after the midnight firing of Willie Randolph in June 2008. The Mets then went 55-38 the rest of the way but missed the playoffs with a loss in the last game at Shea Stadium, on the final day of the season. It was their second consecutive September collapse.
Still, Minaya was given a three-year contract extension through 2012 and Manuel a multiyear deal.
Minaya won't be staying on in another capacity - as of now.
"The fact is that it's not fair to give me another role. If you're going to bring in another GM - first of all, I don't think the GM would want to have me aboard and vice versa," he said. "Whoever the GM is, I would have to make the decision if I want to work with that person."
He said the possibility of talks for a different job with the Mets were for a different day.
"We came to a mutual agreement that at some point in time we might discuss that," he said.
Minaya overhauled a wretched bullpen in the offseason, seemingly the club's biggest weakness, and Sports Illustrated picked New York to win the 2009 World Series.
But long-term injuries to Jose Reyes, Carlos Beltran, Johan Santana, Carlos Delgado, Jason Bay and Francisco Rodriguez have decimated the Mets' roster the past two seasons.
They finished 70-92 last year, their first at $800 million Citi Field, and a promising start this year was all but wiped out by a 2-9 road trip immediately after the All-Star break.
Attendance dropped at the new ballpark, and Rodriguez embarrassed the organization when he was charged with third-degree assault and second-degree harassment following a fight with his girlfriend's father outside a family lounge at Citi Field on Aug. 11.
On the field the Mets went for long stretches without Bay, Beltran, Reyes and Santana, who had shoulder surgery in September that could keep him out for much of next season. And while All-Star third baseman David Wright rebounded from a dreadful season in '09, he struck out a career-high 161 times and slumped for several extended spurts.
Once the Mets dropped out of contention, the decision to fire Manuel was expected.
Manuel, AL Manager of the Year in 2000, is the seventh manager to lose his job this year. Baltimore's Dave Trembley, Kansas City's Trey Hillman, Arizona's A.J. Hinch, Florida's Fredi Gonzalez, Seattle's Don Wakamatsu and Milwaukee's Ken Macha also were dismissed.