Speaking about the European refugee crisis, O'Flaherty called it a "crisis of migration policy" and criticized the failure of EU member states to share the responsibility for tackling it.
As director of the EU Fundamental Rights Agency (FRA), he and his organization have monitored and reported regularly on conditions for refugees in so-called "hotspots."
"We have to be a more welcoming Europe not for everybody but for those who need international protection once they get here," said O'Flaherty.
"And by the way, we aid people to get here in the Mediterranean by a dramatic level of sea rescues which I think is under-acknowledged. But still we have too many walls. Once they get here they have to be treated with respect. We're still not there."
'The thousand small steps'But the refugee crisis continues to strain the sinews of the European project and it is not only populists who are seeking electoral advantages from the turmoil.
Did O'Flaherty recognize the difficulty, therefore, of his organization reporting on the condition of human rights in Europe to governments who may be quite happy with things as they are?
"I'm not going to give Europe a clean bill of health. The problems are serious, the issues are grave, but I do see small chinks of light," O'Flaherty told DW's Michel Friedman.
"I've seen refugees' children locked in cages when I first went to the hot spots in Greece a couple of years ago. They're not in cages anymore. That's an improvement. It's the thousand small steps that are making an important contribution to a better European future."
An EU of rightsBut Europe's problems with human rights exist within its borders too.
At the agency's headquarters in Vienna, O'Flaherty told Conflict Zone: "We have a threat [to European human rights] because of unacceptable levels of abuse ... a pulling away from the commitments in too many places. And on top of that a lack of conviction in large parts of our citizens that human rights are important for them and not just for others."
Countries in Europe with longer democratic traditions are also testing the limits of human rights in the bloc.
In Spain in 2016, two puppeteers were jailed after a show at a carnival in Madrid which the Spanish Interior Minister said had glorified Basque terrorists and humiliated victims, but were freed four days later. In 2017, a dozen members of a hip-hop group were sent to prison for two years each by a high court for "praise of terrorism" in a song.
"We're not an economic Europe, we're one founded in human rights," O’Flaherty told Conflict Zone.
"And if we can better embed that culture, better engage it with the policymakers, then exactly the types of situation you are giving [in Spain] will be much rarer in the future."
A positive impact on rights?So, with all the problems the EU faces on protecting its human rights, does O'Flaherty believe his agency has made a positive impact on rights in the bloc?
"Since this agency has come into existence, we have adopted in Europe a charter of fundamental rights which has hard-wired protection of human rights into policymaking and I see on a day to day basis how the outcome is better because of the charter," said O’Flaherty.
As an advisory body, the FRA has no enforcement powers and relies on politicians acting on their recommendations and warnings.
In a world beset by populism and fake news, that has been something that can not be taken for granted.