Kroos joins Karim Benzema, Jesus Vallejo, Mateo Kovacic, Theo Hernandez and Marcelo on the list of players who are out with injuries.
The reason for Kroos' absence is not yet known and 'Los Blancos' are yet to comment on the issue, but it is more negative news for a team struggling for form.
Despite taking no part in the clash against Real Sociedad, the German midfielder played the full 90 minutes in the shock loss to Real Betis on Wednesday, only throwing more doubt over why he would miss a regular training session.
Marcelo, another of Real's regular starters, is set to undergo some tests and scans to determine the extent of his injury today.
The bad news leaves Zinedine Zidane with a depleted squad for his team's upcoming games. He looks set to be without a recognised striker and a midfield maestro for Saturday's clash against Alaves.