There has been speculation of a managerial move for weeks due to the Orioles' 13 losses in their last 15 games, and Flanagan said the losing stretch was a sign that something had to change.
"It was a tough homestand and a tough month, maybe some of the most horrific losses that this club has ever endured," Flanagan said. "There's been a level of frustration on our parts, and we just felt, after our last homestand, that it was time to make a change."
Flanagan wouldn't comment on ESPN.com reports that he has been in contact with former Marlins manager Joe Girardi as a possible replacement for Perlozzo or that he had spoken with former Chicago Cubs president Andy MacPhail about joining the organization as the chief operating officer.
Flanagan repeatedly called Trembley an interim manager, but would not go into further details about the team's plan. Trembley spent four years as a manager in the Baltimore Minor League system, and this is his first season with the Orioles.
"He has tremendous experience," Flanagan said of Trembley. "I think he was voted one of the five best managers in the last 20 years in the Minor Leagues. He's had a lot of success in the past. He's an experienced guy and he knows how to handle a club."
As for Perlozzo, who was in his third season with the Orioles and 12th year with the organization, Flanagan said he was asked to remain with the team in another capacity. Perlozzo was 122-164 as Baltimore's skipper.
"I don't think we want to get into a game-by-game analysis of his managing skills. We have to look at the overview, and that was the determining factor," Flanagan said. "It wasn't one event, one game that led to this decision. For us, we felt that it was slipping away from us, that we're a better club than we've played and we can still be a better club. But it's been an awful, awful tough run."
Perlozzo will take a few weeks before he makes a decision on his future with the organization.
"As you might imagine, today has been a very difficult one for me and my family," Perlozzo said in a statement. "I am very disappointed that I will no longer be managing the Orioles. That being said, I wish them nothing but the best. I have been with the team for 12 seasons and I consider myself an Oriole. I believe that I have represented the club well during my time with them and I hope that the fans believe that, too."
Following the latest loss Sunday, Baltimore veteran Kevin Millar sounded off about the team's struggles to the media and said he was calling for a players-only meeting before the Orioles start their six-game road trip in San Diego.
"It's frustration," Flanagan said. "Those sorts of things are an indication that things aren't going well with the ball club. I personally think that you don't get a lot out of the team clubhouse meeting. This is the thing we want to get back to, where everybody's on the same page."
The team bus from Camden Yards to the airport was delayed so Flanagan and Jim Duquette, vice president of baseball operations, could meet with the club to discuss the developments.
"We don't feel like we're in limbo," Flanagan said. "Today's steps are in the right direction. We feel like the clubhouse is fine. What we worry about is the morale of the club the last couple weeks going through these very difficult losses. Everything gets wound up tighter, and we felt like it was time to loosen that spring."