25-year-old Pasalic has spent two seasons on loan at the Bergamo club, who now have the option to buy him for €15m (£13.4m).
The Italians are in ‘feverish contact’ with Chelsea trying to get a discount on the €15m.
Chelsea already agreed to reduce Pasalic’s loan fee and are now being asked for another discount.
Pasalic has given his approval to move to Atalanta on a permanent basis.
He has agreed terms with Atalanta for a four-year contract worth €1.5m-per-season plus bonuses.
Chelsea signed Pasalic from Hajduk Split in 2014, but he has never made an appearance for the side.
Instead, the Premier League side have loaned Pasalic out to Elche, Monaco, AC Milan, Spartak Moscow and Atalanta.
Pasalic has made 34 appearances for Atalanta this season, scoring seven and assisting seven goals.