"It is important that the channels of communication, contact and cooperation between Europe and Turkey remain open," Tsipras said.
His remarks followed the European Parliament's approval on Thursday of a non-binding motion to freeze EU-membership talks with Turkey.
"Especially, we firmly protect our belief on this issue at this difficult time," Tsipras said.
He added the agreement between Turkey and the EU should be "completely" implemented even though it was "difficult" and "fragile".