"Saving lives is more important that protecting borders," Francois Crepeau told a press conference following a three-day visit to Italy.
"The migrants will come anyway."
Crepeau said he feared the end of Italy's Mare Nostrum search-and-rescue mission would mean more migrants dying in their bid to reach Europe in overcrowded, rickety boats.
The Italian navy said Friday that 16 bodies had been found in a packed inflatable dinghy found drifting off the island of Lampedusa a day earlier.
The migrants had died of hypothermia and dehydration, the navy said. One of the 76 migrants rescued alive died shortly afterwards.
In October, Italy announced it was ending a costly operation to comb the seas for boats in distress. Rome handed responsibility for the search to the EU agency Frontex.
Crepeau said the Mare Nostrum patrols, which saved over 150,000 lives, had been "very courageous" on the part of the Italian government because it was done despite little backing from the Italian public or from other European nations.
"I came here to see how this change of attitude could be used and expanded to the rest of Europe," he said.
In the long run, he said, Europe would have to come up with a common policy on resettling refugees.
"It would be much better if we … registered everyone, and distribute the refugees among the different countries of Europe," he said.
He also called on EU leaders to jointly develop legal channels for low-skilled migrant workers.
"No politician can say it but we need them to pick up tomatoes or care for the elderly."