UN High Commissioner for Refugees Antonio Guterres said the current EU scheme to share out 160,000 refugees from Italy and Greece over the next two years had to be broadened and "more legal opportunities" had to be provided to exiles.
"You cannot have a technocratic approach to relocation," he told a news conference in Athens.
"Without a human approach to relocation, this process could fail," he warned.
Guterres had just completed a three-day visit to Greece, where he visited registration camps in Athens and on the island of Lesbos, one of the main landing points for migrants fleeing war and misery in the Middle East and Asia across the Aegean Sea from Turkey.
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Over 600,000 people have arrived in Europe this year and with winter looming, the rate seems to be increasing.
The International Organisation for Migration said Friday that there had been a sharp increase in the number of migrants arriving in Greece, to some 7,000 a day, up from 4,500 per day at the end of September.
Only Syrians, Iraqis and Eritreans are currently eligible for resettlement under the EU relocation programme.
Afghans, whose country is also in conflict, are excluded.
Guterres today said the scheme remained vulnerable to "ethnic or religious discrimination," with Slovakia and Cyprus already declaring themselves a preference for Christian refugees.
Guterres said what was needed was "a mechanism that is humane, that is based on dialogue, that is based on persuasion. That is not yet in place," he said.
"You cannot just look into people and say 'you go to Germany, you go to Sweden, you go to Romania, you go to Portugal, you go to Spain' without having a process of information of taking into account the interests, for instance family, links, preferences," he added.
The UNHCR said it was already aware of a refugee family that turned down an offer to relocate to either Lithuania, Finland or Luxembourg.