The migrants -- mainly from Pakistan, Somalia, Morocco, Algeria and Bangladesh -- will be sheltered in disused Olympic stadiums, police said, adding that some 350 riot officers were mobilised at dawn for the operation.
Humanitarian workers had been asked to leave the area while reporters and photographers, some of whom were briefly detained, were held back at a distance of about three kilometres (two miles).
Police said media were moved away "to ensure their protection".
reece and Macedonia are both on the migrant trail that has seen hundreds of thousands of people, fleeing war and poverty in the Middle East and elsewhere, head to northern Europe this year after landing from Turkey in flimsy boats.
UN refugee chief Antonio Guterres on Wednesday called Europe`s refugee situation "chaotic" as he visited a refugee centre near the Finnish capital Helsinki with Secretary General Ban Ki-moon.
"The present chaotic situation with people moving across the Balkans and then coming essentially to three or four countries -- Austria, Germany, Sweden and Finland -- is not sustainable," Guterres said.
"Many European countries are not doing their part of the job," he added, calling for a fairer distribution of the influx.
The EU is planning to distribute 160,000 asylum-seekers across the bloc under a quota system as it struggles to cope with its worst migration crisis since World War II, but is facing legal challenges from Hungary and Slovakia.
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