In the footage, which was distributed by Turkish authorities, one of the guards can be seen pushing the migrant dinghy away with what looks like a metal rod.
Migrants can be heard shouting as the guard uses the rod to beat them back while another shoots into the air, before the coast guard vessel speeds away.
In a statement to journalists, a Turkish official said Greek coastguards "performed manoeuvres aimed at sinking the rubber boat."
The shocking video comes shortly after reports on Monday that a child died when a boat carrying 48 people capsized off the Greek coast.
Until now, Turkey had been preventing migrants from crossing into Greece under a deal signed with the EU in 2016. The decision to let them cross came following escalating hostilities in the Syrian province of Idlib where more than 30 Turkish soldiers were killed by a Syrian airstrike last Thursday.
Comment: See: 33 Turkish soldiers killed in Idlib airstrike as Erdogan chairs emergency meeting with US & NATO on Syria
Police fired tear gas at migrants attempting to cross the land border on Monday after Athens promised that it would implement a policy of maximum "deterrence" at its border and accused Ankara of using migrants "as pawns to exert diplomatic pressure."
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