Modric and Kroos have formed a strong partnership in midfield for Madrid this season, but the bond will be broken after news of the former's injury.
Reports have suggested Modric could miss as much as three months of action.
Kroos says replacing him in midfield will be tough for the Liga leaders, despite Carlo Ancelotti having the likes of Sami Khedira and Asier Illarramendi ready to step in.
"I think that's really hard for Real Madrid to deal with," the Germany international said of Modric's injury.
"He has played almost every game this season and was in great shape and great form.
"It'll be difficult for us to replace him in our next match.
"We hope that he will come back soon although I don't know exactly how long he will be out. However I have to say that for us it's definitely bad news."
Madrid return to league action on Saturday with a trip to Eibar, looking to extend their 13-game winning run in all competitions.
