Conway has impressed during the three months he has spent at Brighton, with Saturday's trip to Middlesbrough the last game before he returns to Cardiff.
Barnes admitted that the final decision was the club's, but said that Conway was a "fantastic player" that Brighton would miss.
"Craig is a fantastic player," he told The Argus. "He has got great quality. He was at Cardiff and they didn't sign him for no reason.
"They got promoted and he was a big part of that last season. It would be great if he could stay but obviously it's about what he wants and what the clubs want."
Brighton are currently 10th in the Championship.