The dispute ended up in the courts and has weakened the bloc’s unity, spilling over to other policy areas.
European Union interior ministers are now struggling with the politically charged issue of reforming the union’s asylum system.
Former communist states continue to defy pressure from other European capitals to accept refugees travelling across the Mediterranean which would ease the burden on nations such as Greece and wealthy destination countries like Germany.
Ms Cretu, who oversees the cohesion policy, highlighted recent investments on the frontlines of Europe’s migrant crisis – from the purchase of two rescue boats for Italian authorities to a support network for mayors of cities wrestling with migration.
When residents and migrants clash, ‘mayors are in the middle’, Ms Cretu said, citing the tiny Greek island of Chios, where arrivals of refugees and migrants have risen recently.
The European Union is using a new approach to measure inequality, which should give policy makers a better understanding of which areas are most in need, according to Cretu.
She said: ‘GDP per capita is not very accurate because it doesn’t take into account these pockets of poverty unemployment.’
Ms Cretu also believes that while the cohesion policy’s biggest achievements to-date have been in traditional infrastructure, basic needs have been neglected in many parts of eastern Europe.
She said: ‘We have still people who are dying because of the quality of water, because the networks were built 40-50 years ago.’