The Greek and Turkish Cypriot leaders sit down to reunification talks in Geneva this week, although both have sought to temper hopes of a swift breakthrough.
Juncker said the current talks were the "very last chance" to reunite the island.
"It's risky, but when it's about peace you have to take risks. When it's about peace, those that take no risks are taking the greater risk," he told a news conference in the Maltese capital.
"I think the time has come to reunite the island. The leaders of the two communities were doing an excellent job and I hope that we will be able to conclude in a positive way the Geneva talks tomorrow," Juncker said.
(Reporting by Alastair Macdonald, writing by Philip Blenkinsop, editing by Gabriela Baczynska)
