Spurs captain Son Heung-min and two other players, the last to line up for individual medals, were left empty-handed after their team beat Manchester United 1-0 to win the club's fourth European title on Wednesday.
Son lifted the trophy without a medal around his neck.
“To our great displeasure, we did not have enough medals available on stage during the trophy ceremony presentation due to an unexpected discrepancy in the player count ..." British media quoted European football's governing body as saying on Thursday.
"More team members – including injured players – participated in the ceremony than initially anticipated.
“The missing medals were promptly delivered to the winning team in the dressing room, along with our sincerest apologies for the oversight.”