The French club's president had claimed the Serie A side submitted an £11.8m bid for the Morocco international, but the Nerazzurri have moved to quash such speculation
On Wednesday, Montpellier president Louis Nicollin revealed his side have accepted Inter's €14m (£11.8m) bid for the Morocco international and have rejected Fenerbahce's offer.
But Inter have subsequently denied Nicollin's claims and insists they have not lodged an official bid for the 22-year-old.
"Sorry to contradict the president of Montpellier, but Inter has never submitted a bid for his player Younes Belhanda," Branca said.
Inter are in the market for a new midfielder following the departure of Wesley Sneijder to Galatasaray earlier this week, but the move could also pave the way for the departure of Philippe Coutinho, with Liverpool keen on the 20-year-old.
A delegation from the Premier League side, including managing directory Ian Ayre, flew to Milan on Wednesday hopeful of tying up a deal.