"The risk is great. The success of the pact so far is fragile. (Turkish) President (Tayyip) Erdogan has several times hinted he wants to terminate the agreement," Juncker told Kurier when asked if the pact could fall apart.
If that happened, "then you can expect that again refugees are standing at the gates of Europe," he added in an interview published on July 30.
Turkey has so far lived up to its side of the landmark deal with Brussels to stop illegal migration to Europe via its shores, in return for financial aid, the promise of visa-free travel to much of the bloc and accelerated talks on membership.
But Ankara has complained Europe is not living up to its side of the accord and has alarmed EU leaders by cracking down on Erdogan's opponents, especially in the wake of a failed coup on July 15-16.
Juncker reiterated his concern about political developments in Turkey and repeated that any move by Ankara to introduce the death penalty would lead to the immediate breakdown of negotiations on joining the EU.