Speaking on Monday, he likened the European project to a "broken compass."
Potočnik, who was in charge of the environment dossier at the Commission from 2010 to 2014, said, "The EU is in a fragile state and we clearly need more transparency, trust and honesty."
His comments come ahead of a summit of EU leaders in Bratislava on 16 September, where they will discuss the future of Europe and the impact of Brexit.
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Potočnik, speaking in Parliament, said the Brexit result which will see the UK exit the EU once article 50 has been triggered, meant the rest of Europe now had to "wake up" its young people.
"We are on a troubled journey and we are going to need their energy and enthusiasm," he said.
Potočnik was attending a hearing on the car emissions scandal.
His comments came on the day UK MP David Davis made his fist statement to the UK House of Commons as Brexit Secretary.
He said that Brexit is "about seizing the huge and exciting opportunities that will flow from a new place for Britain in the world."
British MPs also debated a public petition calling for a re-run of the EU referendum, which has attracted more than four million signatures.
Elsewhere, European Commission President Jean-Claude Juncker, speaking of the Bratislava summit next week, said, "Brexit will not be the major subject and the major issue when we will meet in Bratislava. We have to discuss the future of the European Union at 27."
Meanwhile, a new survey has found that 59 per cent of people believe that the UK is on the right track, however, 71 per cent of those that voted remain in the referendum believe it is not. 57 per cent said they believed the UK economy would do well over the next year. The poll also found that 81 per cent believed that the UK continuing to pay into the EU budget post Brexit would not be compatible with the outcome of the referendum.
Similarly, 79 per cent said giving EU nationals the automatic right to live and work in the UK would not be compatible.
However, 77 per cent said allowing those already living in the UK to stay would be.