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The Amsterdam outfit paid €22.5 million to draft the Ivorian in from West Ham in the January window and he notched twice and assisted four in his first six Eredivisie games.
But bizarrely, it's been confirmed by Ajax that the former Frankfurt striker was omitted from their European squad due to an error and he is set to be unavailable.
Ajax face Lille in the round of 32 this month, having finished third in their Champions League group and been demoted to the secondary competition.
"He is indeed not on the list, we are trying to find out what went wrong," Ajax spokesman Miel Brinkhuis told AD.
"We have contacted the KNVB and UEFA."
At this point it isn't clear if Ajax, the Dutch FA or UEFA were responsible for the mistake. If it is Ajax's fault, they will not be able to amend and must carry on without their star striker.
The deadline for the 25-man squad list was on Wednesday.
After signing Haller, Ajax allowed veteran striker Klaas-Jan Huntelaar to return to former club Schalke in a decision they might now live to regret.
Even without playing as the club's first-choice frontman, the 37-year-old struck seven goals in 14 appearances in all competitions this term.
Ajax's first leg against Lille will be played on February 18, with the reverse fixture at the Johan Cruyff Arena coming a week later.
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