Her remarks, following a EU foreign ministers meeting in Valletta, came after recent calls from some countries that negotiations over Turkey's potential membership of the bloc should be stopped.
The talks in Malta highlighted sharp differences on ties with Turkey after President Recep Tayyip Erdogan's victory in a referendum to reform the constitution gave him increased powers.
Germany urged its EU peers not to end accession talks despite deep misgivings over Turkey's rights record, saying the country is key to European interests, not least as a NATO ally.
After a "very frank and open" meeting with the foreign ministers, Mogherini said she was "happy to have (Turkey) in but a level of clarification" was needed from Ankara.
"The accession process continues, it is not suspended, not ended (although) we are currently not working on any new chapters," she told reporters.
"The criteria are very clear, well known and if Turkey is interested in joining, as the foreign minister told us today...It knows very well what that implies, especially in the field of human rights, rule of law, democracy and freedoms," she said.
The EU backed the losing side but that was in the past and from now on, the EU should "put efforts into how you will develop your relations with Turkey. Although you carried out that campaign, we are opening our door", he said.
Mogherini, who said the EU respected the outcome of the vote, was due to meet Turkish Foreign Minister Mevlut Cavusoglu later today.
German Foreign Minister Sigmar Gabriel said earlier that his government was "strictly against breaking off the accession talks.... It would be the completely wrong reaction."
But Austrian Foreign Minister Sebastian Kurz repeated his call for talks to be halted and told his EU colleagues to make their minds up.
"I consider it completely wrong if we hold up this fiction of an accession (to the EU) as Turkey moves away even further from Europe every year," Kurz said.
"We need, finally, a clear decision."
In March last year, the European Union signed an accord with Turkey to speed up the accession talks, along with visa liberalisation and billions in aid in return for Ankara halting a flood of migrants, mostly from Syria and Iraq, coming to Europe.
The president also warned that he would review relations with the EU as a whole after the referendum.
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