He spoke ahead of an interview Hariri is set to give to a Lebanese satellite channel later today from Riyadh, in his first public comments since his shock resignation on November 4.
Since Hariri's departure, rumours have swirled that he is being held against his will in the Saudi capital.
Aoun on Sunday criticised "the obscure circumstances in which Prime Minister Saad Hariri is staying in Riyadh", a presidency statement said.
The situation has "reached the point where Mr Hariri's freedom has been restricted, and conditions have been imposed regarding his residence and the contacts he may have, even with members of his family," the statement said.
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Aoun has yet to formally accept the resignation of Hariri, who also hold Saudi nationality, and has said he wants to meet him in person to discuss the situation.
After being cautious in his early comments, the Lebanese president has hardened his tone in recent days.
On Saturday, he called on Saudi Arabia to "clarify the reasons that have prevented the return of PM Hariri to Lebanon to be among his people and supporters".
Hezbollah chief Hassan Nasrallah said on Friday that Hariri was "detained in Saudi Arabia" and "banned from returning to Lebanon".