Allen said Thomas had a dislocated second toe and will have surgery to repair it.
"I'm not going to get into any time frames right now. I don't know that," Allen said. "He's going to go on IR. I don't anticipate that he'll be able to return this year."
Thomas has not played in a game since injuring the toe against the Carolina Panthers in Week 3. Allen was asked earlier in the season why Thomas did not go on injured reserve at the time of the injury and the coach said the initial timetable potentially put the receiver's return around the four-game mark, noting that it was a tough decision to place a "player of that caliber" on IR if there was a chance he could come back ahead of schedule.
Allen had said last week that he believed Thomas and wide receiver Jarvis Landry, who hasn't played since the Saints' game against the Minnesota Vikings in London in Week 4, would play again this season. But, according to Allen on Thursday, recent tests indicated Thomas was not healing as expected.
"I don't think there was any complication," Allen said. "I think we followed what the doctors recommended in terms of trying to rehab it and give him an opportunity to play through it. We went in and had another MRI the other day, and it hasn't healed the way that everybody was kind of hoping it would. And so surgery is the next option."
Allen said that Thomas was disappointed because "he put a ton into this to try to get himself back."
"I think Mike worked his tail off and did everything he possibly could to try to rehab it," Allen said. "This is just something that happens from time to time. It didn't respond the way we wanted it to, so we felt like surgery was the best option to go ahead and repair it and try to get him healthy."
Quarterback Andy Dalton said: "Ever since I've been here and been in this building, he does everything he can to make sure that he can put himself in the best possible situation. It's unfortunate through the last couple of years that he's had the injuries he's had, but sometimes it just happens that way. But he's a guy that will do anything in his power to try to get back."
Running back Alvin Kamara was disappointed that Thomas is out for the season and strongly defended his teammate.
"It just sucks to have a player of that caliber, an elite player that obviously works hard, and is passionate about the game, that just kind of got hit with some unlucky things. I just saw a couple of comments in the media about him. Basically like, 'You can't trust him. He's not being honest about his injury, why is he waiting until now to be ruled out?' I'm like, man, nobody knows what we go through in here," Kamara said Friday. "The masses get to see Sunday. It's a lot of s--- we've got to go through. A player like that, that's fighting to get back, not only for his team, but for the fans and for this city ... for people to be talking s---, it's like, ah, it hurts my soul to see that."
Thomas signed a five-year, $100 million extension prior to the 2019 season, a campaign in which he set an NFL record with 149 catches and was named the Offensive Player of the Year. He has missed 31 games since the beginning of the 2020 season.
Complications from an ankle injury in the 2020 opener caused him to miss the entire 2021 season. While there was some hope he could return last year, Thomas announced Nov. 3, 2021, that he would not return because of a "small setback."
Thomas had a public feud with the team last summer over the timeline of his surgery to repair a torn deltoid and ligaments in the injured ankle.
"We can put [the 2021 surgery timetable] to rest right now," Thomas said in July. "It's pretty much like when you go to a doctor, you get an opinion. You go to two doctors, one person has an opinion, another person has an opinion. You have the right to pick an opinion. So if one of the opinions is you can rehab your ankle and it should be good by camp, and I've never had surgery, then I'm going to stick with that one. If that one doesn't work, then I'm going to go with the second one. And that's pretty much how it worked. I don't write the opinion; I just have to pick one."
Thomas looked back in form to start this season, catching 16 passes for 171 yards and three touchdowns in his first three games, including two touchdowns in the opener against the Atlanta Falcons. He was 5-for-5 in receptions against the Panthers before exiting with the injury late in the game.
"Obviously, we know what Mike has been able to do in this offense and we'd love to have him out there," Dalton said. "But for him, the most important thing is getting healthy at this point."
Thomas, a second-round draft pick for the Saints in 2016, has caught 526 passes for 35 career touchdowns and 6,121 yards. He was named to the Pro Bowl from 2017 to 2019 and was first-team All-Pro in 2018 and 2019.