Los Blancos fell to a second defeat in three games on Saturday as Villarreal ran out 1-0 winners at the Bernabeu.
Real now sit 16 points behind league leaders Barcelona in the table, and Kroos conceded that the gap between the two bitter rivals will be difficult to surmount.
"We have to focus on qualifying for the Champions League next season," the German told beIN Sports. "We have to think about our current position. I think this should be our goal for the remainder of the season."
"Sixteen points is very far away and now isn't the time to think about anything other than the next game. We have to start gaining points once more. This will allow Real to get closer to their goal of finishing inside the top four."
Real return to La Liga action next Sunday with a home game against Deportivo La Coruna.