The purge that has seen over 35,000 people arrested as well as some journalists and MPs put in jail had raised questions over the future of Turkey's accession effort, which dates back to the 1960s.
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However, German Foreign Minister Frank-Walter Steinmeier said, after talks at Ankara with Turkish counterpart Mevlut Cavusoglu, he did not support halting accession talks with Turkey.
"The question of whether Turkey goes closer to, or further away, from Europe is not a decision for Europe or the European capitals but should be made in Turkey," Steinmeier told reporters.
"I am for a better relationship," he added.
Steinmeier said his talks with Cavusoglu had "not been easy" and admitted the pair had expressed "divergent views" about the crackdown in Turkey.
But he insisted that Ankara should not see criticism from Berlin as "being lectured or disrespect for its sovereignty", saying it was in the interest of long-term relations between the two sides.
The comments came a day after Turkish President Recep Tayyip Erdogan warned the EU to decide by the end of the year on the membership bid, threatening to otherwise call a referendum on the process.
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Steinmeier said he was "to say the least irritated" by repeated criticism from Erdogan accusing Germany of harbouring wanted Kurdish militants.
Cavusoglu added that he was tired of what he described as "two-facedness and double standards" from the European Union.
"We are fed up, we really are fed up with this condescending attitude," he said.
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