"We are the ones saying today rule of law has to be protected in the country, there is no excuse for any steps that take the country away from that," Mogherini said as European Union foreign ministers met in Brussels.
"As we have been the first ones to say that in that tragic night (of Friday's coup attempt), the democratic and legitimate institutions needed to be protected," she told reporters.
Would-be EU member Turkey carried out fresh raids on Monday as the EU ministers were meeting, prompting growing international concern over the scale of the crackdown.
Judges and military commanders are among 6,000 people who were arrested over the weekend as President Recep Tayyip Erdogan vows to stamp out the "virus" of the coup plotters.
The EU commissioner dealing with Turkey's long-stalled bid for membership of the bloc meanwhile said it appeared that the government had already prepared a list before the coup of people to be rounded up.
"I mean, the lists are available already after the event indicates that this was prepared and at a certain moment should be used," EU enlargement commissioner Johannes Hahn told reporters.
Turkey's attempts to join the 28-nation European Union have been hobbled in recent years by concern over the increasingly authoritarian Erdogan's record on human rights and press freedom.
But the EU agreed to speed up its membership bid and give visa-free travel to Turks as part of a migrant crisis deal in which Ankara agreed to take back people landing in the Greek islands.
French Foreign Minister Jean-Marc Ayrault said that "the rule of law must prevail".
"France has condemned the coup, you can't accept the military taking power," he said. "At the same time we have to be vigilant that the Turkish authorities don't put in place a system which turns back democracy."
Belgian Foreign Minister Didier Reynders also urged restraint, saying: "It's normal to punish those involved in the coup, but it's normal to ask for respect for the rule of law."
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