According to Calciomercato, the centre-back declined to join the squad for matches against Turkey on November 12 and Italy three days later.
Despite being a regular starter for Milan, De Winter has not featured in any of Belgium's four Nations League group matches this campaign.
Van Bommel addressed the defender's decision during Friday's squad announcement, raising concerns over his international future.
"Koni De Winter is absent because he didn't feel comfortable in his situation and decided not to come. It's his choice, I can't do anything about it," he told the media.
"I spoke to him and explained the situation, as a coach, a former player and a father.
"You have to accept it, but it has long-term consequences. He's 24 and he's a responsible person."