The Netherlands decided in July to ban Israel's far-right Finance Minister Bezalel Smotrich and the ultra-nationalist Security Minister Itamar Ben-Gvir.
Veldkamp announced this week that he wanted to see expanded sanctions in response to Israel's planned invasion of Gaza City.
I feel limited when it comes to being able to set the course I consider necessary as Foreign Minister, he said when he announced his resignation late on Friday.
Veldkamp's party, the conservative NSC, is simultaneously withdrawing from the already fragile governing coalition.
Extensive protests in the Netherlands against Israel's actions in Gaza have demanded tougher measures from the government's side.