"Let's not change the referendum into a vote about Europe," Juncker told the authoritative NRC daily newspaper in an interview published today, according to the report.
"I sincerely hope that (the Dutch) won't vote no for reasons that have nothing to do with the treaty itself," he added.
Should Dutch voters oppose the deal, Russia "stood to benefit most," Juncker said, according to the report.
The 2014 association agreement provisionally came into effect on January 1 and nudges the former Soviet bloc nation towards eventual EU membership.
Dutch Prime Minister Mark Rutte has said his government was bound by law to hold the referendum, and would afterwards assess the results to see if any change in policy was merited.
As is known, a referendum on the approval of the Association Agreement between the European Union and Ukraine will be held in the Netherlands on April 6, 2016. The referendum question will be: "Are you for or against the Approval Act of the Association Agreement between the European Union and Ukraine?"