Others were with their families in overcrowded detention centres, where inter-communal frictions and contradictory information created "an unacceptable level of confusion, frustration, violence and fear", he said.
"Children should not be detained - period," said Crepeau, on a fact-finding mission in Greece from May 12-16.
"Detention should only be ordered when people present a risk, a danger, a threat to the public and it has to be a documented threat, it cannot simply be a hunch."
Crepeau said children and families should be offered alternatives to detention. He urged authorities to develop a "substantial and effective" guardianship system for unaccompanied minors and increase the shelter capacity for them.
More than a million migrants, many fleeing the Syrian war, have arrived in Europe through Greece since last year.
More than 150,000 have arrived in 2016 so far, 38% of them children, according to UN refugee agency data.
Greece, in its sixth year of economic crisis, has struggled to cope with the numbers.
International charity Save the Children says an estimated 2,000 unaccompanied children who travelled alone to Europe or lost their families on the way are stranded in Greece and only 477 shelter spaces are available across the country.
