Only 38.1 percent of Dutch voters were in favor of the treaty, BNO said on Wednesday.
Earlier, the national ANP news agency reported citing preliminary estimates that 64 percent voted against the EU-Ukraine agreement on political and economic partnership on Wednesday, while 36 percent voted for.
The referendum turnout has to be over 30 percent in order for the vote to have legal weight.
Dutch Prime Minister Mark Rutte said on Wednesday that the Netherlands could reconsider the ratification of the EU-Ukraine association deal as the majority of the population reportedly says "no" in the Dutch advisory referendum.
The EU-Ukraine Association Agreement, establishing a political and economic association between Kiev and Brussels, was signed in 2014. The Dutch government decided to hold a non-binding referendum after over 400,000 people signed a petition to put the matter to a nationwide vote.