Southampton were expelled from the Championship playoffs after acknowledging they observed opponents' training sessions within 72 hours of matches, with Middlesbrough reinstated on Tuesday to face Hull City in Saturday's final.
The winner of the lucrative playoff final, often described as the richest match in soccer, is promoted to the Premier League next season.
"We will now investigate, and won't comment further until we have assessed the evidence," the FA said in a statement.
The club have also been handed a four-point deduction for next season, while their appeal, which argued the punishment was "disproportionate", was rejected on Wednesday.
The English Football League (EFL) confirmed on Wednesday that the club's sanction, along with a four-point deduction for the 2026–27 season and a formal reprimand, will stand, forcing the south-coast side to quickly turn its focus to rebuilding both on and off the pitch.
The club had admitted to spying on opponents in a case dubbed 'Spygate', including filming a Middlesbrough training session before their semi-final, as well as similar incidents involving Oxford United and Ipswich Town earlier in the campaign.