As veteran Dayne Zorko nears full fitness, former West Coast co-captain Allen faces 12 to 14 weeks on the sidelines with a foot fracture.
The key forward hurt his right foot late in the last quarter of the reigning premiers' round-seven win over Adelaide and is scheduled to have surgery this week.
Allen's final season at the Eagles was cut short due to knee surgery, the 27-year-old managing just 12 games.
The key forward had damaged his calf and Achilles in West Coast's round-14 loss to Carlton, before opting to have patella tendon surgery to fix an ongoing issue with his left knee.
He had also missed the entire 2022 season with a foot injury.
Fellow key forward Eric Hipwood is already sidelined and is not expected back until halfway through the season.
Key defender Darcy Gardiner (shoulder) is at least three weeks away, while midfielder Jarrod Berry (calf) is sidelined for two-to-three weeks.
Featuring in all seven games so far, Allen has kicked 12 goals to help the fifth-placed back-to-back premiers to a 4-3 start this season.
Zorko (calf) has been listed as a test to face Essendon at Marvel Stadium on Saturday, while defender Noah Answerth works through concussion protocols.
Elsewhere, Fremantle expect injury-prone ruck Sean Darcy to miss at least a month after another soft-tissue setback.
While the club doesn't have an exact timeline, Dockers coach Justin Longmuir anticipates a five-week stint, at minimum, for Darcy.
Darcy is managing another flare-up of the same calf he strained in January.
Ruled out of the round-six derby, the 27-year-old was building his way through concussion protocols when he hurt his calf in a rehab session.
"We don't have a timeline, so to speak," Longmuir said on Tuesday.
"But it's a very similar injury to what he did in pre-season, and he missed about five weeks with that.
"We're expecting something along those lines."
It is just the latest of hamstring, calf, knee and ankle issues for Darcy, who had played just 44 games across three seasons before this year.
Former Magpies player Mason Cox has been called up in Darcy's absence to partner star ruckman Luke Jackson, with the Dockers sitting second (6-1) to Sydney on percentage.
Longmuir is hopeful Patrick Voss (illness) will be fit to face the 10th-placed Western Bulldogs on Friday, though he admits the key forward is still feeling unwell.
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