The move comes after Turkish Foreign Minister Mevlut Cavusoglu said he would travel to Rotterdam, despite a ban on him addressing a rally there.
The Dutch are due to vote in a national election on Wednesday, in which anti-immigration sentiment has played a prominent role.
Rutte said in a statement published on his official Facebook page that Turkey had upset discussions under which Cavusoglu would have been allowed to enter the country, by calling for a massive public rally.
A Turkish threat of sanctions if Cavusoglu were denied entry "made a reasonable solution impossible", Rutte said, Reuters reported.