"We want the rule of law to work properly in Turkey," Jean-Marc Ayrault told France 3 television, warning Turkey's government against "purges".
His remarks came as Turkish authorities continued a crackdown over the coup, arresting over 6,000 people accused of involvement in the putsch or of supporting the coup plotters.
Ayrault said the events of the past two days had raised questions about Turkey's "reliability" in the fight against Islamic State.
Turkey is a member of the US-led coalition that has been carrying out airstrikes against the group in Syria.
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