Ukraine, which joined the World Trade Organisation in 2008, shocked the global trade body last September by announcing plans to raise tariff ceilings on 371 goods using a rule that other nations say should be reserved for minor adjustments.
At a WTO meeting last December, more than 120 out of 157 WTO members - including the EU, the United States and China - condemned Kiev's move which would raise protective barriers around its car industry, agriculture and other sectors.
However, Ukraine's chief trade negotiator Valery Pyatnytsky this month dismissed such criticism as "bullying" and said Kiev would press ahead with its plans.
The EU responded with an ultimatum.
"We have made our views quite clear on all occasions in formal and informal contacts with the Ukrainian authorities in Brussels, in Geneva and in Kiev and we repeat it again now: it would be in the interests of all WTO Members for Ukraine to withdraw its notification," the EU delegation in Ukraine said in a statement.
"We also wish to emphasise that Ukraine's actions ... act against Ukraine's own stated interests in signing and ratifying the EU-Ukraine Association Agreement and the DCFTA (Deep and Comprehensive Free Trade Agreement). It is difficult to reconcile this notification with the letter and the spirit of the DCFTA."
Kiev and Brussels first planned to sign the deals - which are packaged together - in late 2011 afters years of tough negotiations.
But the EU put off the signing after a Ukrainian court jailed former Prime Minister Yulia Tymoshenko, President Viktor Yanukovich's key opponent, on abuse-of-office charges which Brussels saw as politically motivated.
This year, Brussels tentatively scheduled the signing for November, setting out conditions including legal reforms.
Thursday's warning added another item to that list, increasing the risk that the deal will fall through again as Ukraine appeared headed for trade protectionism.
Just hours before the EU published its statement, Ukraine's government introduced emergency tariffs on auto imports that will affect supplies from such countries as Germany, Russia, Japan and Korea. (Reuters)