The motion approved yesterday (27 March) says the PVV website (see background) characterises an entire category of people - those from Central and Eastern Europe - as undesirable.
"The Lower House, after having heard arguments, states that the PVV website ... unnecessarily puts a group of people in the cross-hairs," said the motion, approved by a 94-56 vote. PVV has 23 MPs.
The European Parliament has called the website "deplorable" and pressed Prime Minister Mark Rutte to distance himself from it.
The motion was tabled by the central-left D66 party.
"This is the first time the Dutch parliament has collectively spoken out about the website," Daan van Bonenkamp, D66's parliamentary spokesman, told Agence France-Presse. "We have asked cabinet for a reaction."
The motion was backed by the Christian Democratic Alliance (CDA), a junior member of the ruling coalition, as well as by Hero Brinkman, a breakaway PVV member.
Wilders criticised the CDA's vote as "inconsistent, a mistake".
According to Radio Netherlands, D66 leader Alexander Pechtold has sent a letter to the cabinet, asking what it intended to do with the motion condemning the site.
So far, Rutte - from the conservative VVD party - has refused to condemn the website, saying that it is a private initiative by a political party and has nothing to do with his government. However, Rutte's minority coalition relies on Wilders' party to get its legislation through the lower house.
Wilders said the motion was "not very nice," adding, "I don't like it at all".
But he said he does not believe it will have any effect on the budget negotiations between the coalition partners and the PVV. The government needs to cut billions from next year's budget and the PVV's support will be crucial if the measures are to be approved.
CDA MP Eddie van Hijum agreed that the vote against the PVV website shouldn't affect the budget negotiations. "Wilders has the right to start an anti-Polish website and we've got the right to express an opinion about it. He hasn't asked the Christian Democrats to start a similar site," he was quoted as saying.