European countries are facing record numbers of refugees and other migrants entering Greece illegally from Turkey.
Dutch State Secretary for Security and Justice Klaas Dijkhoff said the protesters had crossed a line.
"Finding shelter for asylum seekers poses difficult questions but there is a limit when it comes to expressing your opinion," he said on Dutch TV.
"The line is crossed when you barge in yelling and rioting. That`s not appropriate in a discussion and, thankfully, we have seen that it went much quieter in other places and a solution was found. This is not ok."
The migration crisis is expected to dominate a meeting of EU leaders on Thursday.
Sad `through and through`
Local mayor Miranda de Vries said no-one in the meeting hall had been injured but tweeted she was sad "through and through".
The meeting in Geldermalsen was to discuss establishing a centre for 1,500 asylum seekers.
About 2,000 people joined the protests from the municipality of 27,000, 27 km (17 miles) from Utrecht, Dutch national broadcaster NOS reports. Local police say they made several arrests.
Along with Germany and Sweden, the Netherlands is one of the most popular destinations for migrants in the wealthier north of the EU.
Including this year`s arrivals, the government said last month it expected to receive 58,000 asylum seekers by the end of 2016.
Former prisons, empty government offices and sports halls are being hastily modified to accommodate the surge in numbers.
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