"If such a complex European region gets an impression that we are not serious with the European perspective, we will experience, sooner rather than later, what we saw in the Balkans during the 1990s," Juncker said on Friday.
In the 1990s, the former Yugoslavia, which was comprised chiefly of Serbs, Croats and Muslims, was caught in Europe's deadliest conflict since World War II, marked by many war crimes, including ethnic cleansing and crimes against humanity. A large number of Bosnian Muslim men and boys were systematically massacred by Bosnian Serb forces during the conflicts.
Juncker, who was speaking at the Austrian parliament in Vienna, said the history of the 1990s still has not been overcome in the Balkans.
Only two former Yugoslav states, Slovenia and Croatia, had been accepted by the EU.
Bosnia, Albania, Serbia, Macedonia, Montenegro and Kosovo, which were currently at different stages of accession talks with the European Union, do not feel the EU is serious about offering them future membership.
Membership negotiations have officially started with Serbia and Montenegro. Albania and Macedonia were on the waiting list for accession talks and classified as "candidate countries". Muslim-majority Bosnia-Herzegovina and Kosovo were listed as "potential candidates".
Last December, Juncker announced that expanding into the Balkans was vital to maintain stability on the European continent and he expected Serbia and Montenegro to join the bloc by 2025.
Nevertheless, the road to full EU membership for those states was "still very long," Juncker said.
While some of the countries had made progress, "that progress still hasn't gone far enough."
He suggested that the EU could offer the states a sort of "economic area where they can partially behave as they will eventually do as full member states."
Juncker pointed out that he didn't think any of the six Balkan countries would attain full membership "before 2025, and even then it won't be quick". The EU must "tend to the west Balkans intensively and help where necessary," the EU Commission chief said.
It should "ensure it is understood that all border conflicts between the west Balkan states must be resolved before the membership can be attained," he said.
Among the most pressing issues is the status of Kosovo, which unilaterally declared independence from Serbia in 2008.
Kosovo is currently recognized by 117 countries as an independent state, including the United States and most members of the European Union, or the EU. Five of the 28 EU member countries, namely Spain, Slovakia, Cyprus, Romania, and Greece, have not recognized Kosovo’s independence from Serbia.
Serbia still sees Kosovo as part of its territory and has the support of Russia and China.