The apology is being criticized by Netanyahu's finance minister, the more extreme Bezalel Smotrich, who calls the move a "shame" in a post on X.
Israel's attack, which was directed at Hamas' negotiating delegation in Doha, killed five people and was widely condemned.
Until now, Israel has defended its actions and even threatened Qatar and other countries that it will continue on the same line.
I say to Qatar and all nations that harbor terrorists, either you expel them or put them on trial. If you do not do so, then we will do it, said Netanyahu in a speech shortly after the incident.