"If our neighbours move to significantly liberalise a customs regime with the EU then the Ukrainian market will indeed be flooded by goods whose quality and price are rather good," Putin said.
"This will prompt them to push Ukrainian-made goods out of the Ukrainian market," he was quoted as saying by Russian news agencies.
"Then the countries of the Customs Union will have to think about protective measures, such a possibility exists," Putin said.
The repeatedly-delayed deal would open up EU markets for Ukrainian exports.
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Putin added that a Ukrainian delegation would arrive in Moscow next week to discuss Ukraine's possible signing of the deal and its consequences.
"Next week our Ukrainian colleagues will come to Moscow to analyse on an inter-governmental level all the possible threats related to this situation," he was quoted as saying.
Ukrainian Prime Minister Mykola Azarov will travel to Moscow for talks with his Russian counterpart Dmitry Medvedev on Monday, Medvedev's spokeswoman told AFP.
Ukraine has so far steadfastly resisted the pressure.
Last month Putin travelled to Ukraine for talks with his Ukrainian counterpart Viktor Yanukovych in what analysts described as a last-ditch attempt to persuade Kiev against signing the EU trade deal.
Those talks apparently collapsed, and after Putin returned to Moscow, Russia banned the import of a popular Ukrainian chocolate brand.
Soon afterwards, Russian customs began subjecting all Ukrainian imports to rigorous checks in a move that a top Putin aide, Sergei Glazyev, publicly admitted was a warning to Kiev.
Ukraine's agreement with Brussels has been repeatedly postponed after a Ukrainian court jailed former prime minister Yulia Tymoshenko for seven years in 2011.