The Netherlands is the only country in the 28-nation EU that still has to ratify the agreement, although the deal has been approved by both the upper and lower houses of the Dutch parliament.

Some parts of the Ukraine-EU Association Agreement have been already provisionally applied since Nov. 1, 2014.

Although in the agreement nothing is said about an EU membership of Ukraine, many Dutch people think differently.

According to a poll by opinion poll agency Ipsos, requested by national broadcaster NOS, 46 percent of the Dutch citizens consider the Association Agreement as the first step toward Ukrainian membership of the EU.

Meanwhile, the referendum, initiated by euro-sceptic Dutch, was seen as a protest vote against the EU. Initiators of the vote have admitted that the vote was essentially not about Ukraine but about a broader anti-EU agenda, such as the immigration open border policies.

Calls for a boycott escalated when voters saw that supporters of the referendum were not really interested in the EU treaty with Ukraine, but in stimulating euro-scepticism among the Dutch, according to political scientist Andre Krouwel at VU University Amsterdam.

And since it was the first time that a threshold has been set on a voting procedure in The Netherlands, "it gave impetus for a new dynamic in which members of the electorate could implicitly vote by simply staying at home," said Krouwel.

"The revelations caused confusion and anger among voters, who decided to abstain from voting," he said.

For some experts, even if ratification is reconsidered by the Dutch government, this would not necessarily mean that the rest of the EU will not implement the treaty with Ukraine.

"The Dutch 'No' vote does not automatically terminate the provisional application of the agreement. It may be expected that a compromise will be sought within the Council of the EU to save this part of the agreement, while somehow taking into account the concerns expressed in the Dutch referendum," said Peter van Elsuwege, professor of the EU law at Ghent European Law Institute (GELI).

"The 'No' vote is rather embarrassing for the Dutch government which currently holds the rotating EU presidency. It is also annoying for the EU as such, taking into account the upcoming Brexit referendum and the rise of euro-scepticism on the continent," van Elsuwege said.

According to Dimitrova, it would also give a negative signal to countries seeking association agreements with the EU, while harming the bloc's credibility.

"In countries like the Western Balkans we might see a negative impact on their effort to implement reforms," she said.