Following Sunday's 2-0 defeat by the Norwegians, Kovac accused his players of producing less than a fully committed performance but Modric was quick to differ with his boss.
"That's the coach's opinion but I am totally sure that every player out there left everything on the pitch," Modric told Croatian media.
"Everyone is entitled to an opinion," he said. "We were poor and our game plan fell apart but we still tried our best. Unfortunately, things went in the wrong direction."
The first signs of a rift between the two appeared in Friday's 0-0 draw at Azerbaijan, when Kovac substituted Modric midway through the second half and the Real Madrid playmaker was clearly unhappy with the decision.
The 29-year-old said after the game he had no idea why he came off and added it was a question for Kovac, who has come under strong pressure from local media to step down after a pair of tepid performances.
The results left Croatia's chances of reaching next year's 24-team tournament in France in the balance.
They are third in Group H on a provisional tally of 15 points from eight games, three adrift of leaders Italy and one behind Norway.
Governing body UEFA had deducted a point from Croatia's tally for a racist incident in June's 1-1 home draw with Italy, when the Balkan country's fans carved out a swastika on the pitch with a chemical agent.
Croatia appealed the verdict but if UEFA uphold it at a hearing later this month, they will be reduced to 14 points ahead of their last two qualifiers at home to Bulgaria and away to Malta.
The top two from each of the nine groups and the best third-placed team qualify automatically along with hosts France, while the other eight third-placed teams enter a two-legged playoff for the remaining four berths.
(Writing by Zoran Milosavljevic in Belgrade; editing by Sudipto Ganguly)
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