Reports suggested that PSG were set to activate the Argentine's release clause, reported to be around €250m.
However, the Qatari has denied any interest in Messi, who was recently ruled out for up to two months.
"I haven't spoken to Messi because I'm not interested," Al-Khelaifi told AS.
"You would have to ask the Barca president (if he is available), not me.
"I won't pay what they say he's worth. I'm a realist and that amount is unrealistic," he added.
"I'm not thinking about the possibility at all."