"The nature of his condition requires him to be on blood thinners for several months and he will be unable to play hockey during this time," Avalanche physician Dr. David Mellman said.
Fleischmann, 26, had been expected to play Thursday night against the Nashville Predators, but he was examined in the afternoon after telling head trainer Matt Sokolowski that he was having shortness of breath.
"Our trainers are very attentive to our players' needs and when Tomas went to see Matt, Matt thought he should go see our doctor, and our doctor took it from there and did the necessary tests," Avs General Manager Greg Sherman said. "Fortunately, at the end of the day, this was discovered. He's a young man and obviously this is a serious condition.
"All the indications from our doctor are that he will be able to live a normal life. This is something that can be treated through medications."
Sherman added Fleischmann's condition is "not life-threatening" and that he isn't staying in the hospital.
Fleischmann missed the first 11 games of last season with the Washington Capitals because of a blood clot in his leg.
The loss of Fleischmann is another major blow for an Avalanche team that has lost 231 man games to injuries and illness this season.
"Certainly Tomas was a big piece of our team, but we've dealt with adversity before," Sherman said. "This isn't the first time we've had to deal with injuries to a player this year or last year. The depth of our organization has come through in the past and we expect it to come through here in the future.
"We're not the only team that has to deal with (adversity). We're confident with the personnel that we have and we move forward."
Fleischmann had 8 goals and 13 assists in 22 games with the Avalanche following his Nov. 30 acquisition from Washington in exchange for defenseman Scott Hannan. He finishes the season with 12 goals and 19 assists in 45 games.
Fleischmann was skating on a line with center Matt Duchene and right wing Chris Stewart, who played his third game in Thursday's 5-1 loss to the Predators after missing 21 games with a broken hand. Ryan Stoa, who was recalled Wednesday from Lake Erie in the American Hockey League, took Fleischmann's spot on the line against Nashville.
"Certainly you never want to lose a player like that," coach Joe Sacco said. "Tomas was playing very well for us. He's been a guy that had some production at very important times of the games. He was very clutch for us in many games. We have other people that have to step in there and take advantage of an opportunity. He was scoring and making some big-time plays for us. He'll be missed."
Said Duchene: "Tomas obviously has been one of our best forwards since he arrived. For me, he's been a great linemate. It's tough to lose a guy like that, but we've been a team all year when we've had injuries, we've pressed forward and had other guys step up. We're going to move forward here and hopefully he has a speedy recovery and he gets back as soon as possible."
The Avalanche is battling for a playoff position in the tightly-bunched Western Conference, and Sherman said he would meet with Sacco on Friday to discuss the state of the team.
"This is news that came to light in the last couple of hours," Sherman said. "Certainly we'll sit down with the head coach and have a discussion and assess where we're at. I'm confident in the people we have in the organization, the players we have in the organization. We'll assess where we are and go from there."