The 26-year-old central midfielder joined Mallorca on loan last August in a move that was set to expire in June.
However, Athletic confirmed on their official website that they brought him back to San Mames on Friday.
Perez had not trained with Mallorca this week.
Athletic's statement said: "Athletic have brought back Inigo Perez, who was loaned to Mallorca. The player, who will wear the number three shirt, has been affected by a case of stress. Athletic will do all within their power to help the recuperation of the player."