Messi rocked Barcelona last week when informing them of his desire to leave the club he initially agreed to join as a 12-year-old.
Now 33, Messi had a clause in his contract that allowed him to leave on a free transfer at the end of the 2019-20 season, but that is reported to have expired at the end of May.
But because the coronavirus pandemic extended the season into August, Messi and his entourage believe it should still be valid.
LaLiga has sided with Barca, though that has not stopped speculation as to his next destination from running wild, with Manchester City appearing the most likely move.
Messi's father, who is also his agent, suggested on Wednesday that his son remaining at Barca would be "difficult", and Kroos – a regular opponent of the Barca icon in El Clasico – thinks it would be bad for the league if the Argentinian star left.
"Messi is a player who is interesting for all clubs in the world," Kroos said in a news conference on international duty with Germany.
"It's bad for LaLiga and especially for Barcelona. For me, as a Real Madrid player, it's of course something different.
"But even if Messi left, it wouldn't automatically mean that we at Real Madrid would win everything."
Messi has a year left on his contract at Barca, who are reportedly demanding his €700million release clause be met for their talisman to leave.
Should he depart without playing another game for them then his final match will have been the 8-2 Champions League humiliation to Bayern Munich.