The Real Madrid midfielder was substituted after 62 minutes of his side's 2-2 draw against Czech Republic on Friday, a move which head coach Ante Cacic later attributed to tiredness and muscle tightness.
Cacic was then forced to deny claims by the team doctor that Modric would miss the Spain game through injury, insisting that his substitution had been purely precautionary.
But the 30-year-old was a notable absentee from Saturday's training session, along with Vedran Corluka, Domagoj Vida, Ivan Perisic, Marcelo Brozovic and Mario Mandzukic.
Croatia were leading the Czechs by two when Modric was withdrawn and subsequently lost control in midfield, conceding twice in the final 15 minutes.
Victory over Spain in Bordeaux on Tuesday would see Cacic's men progress as group winners and they will be desperate to have Modric available.