Foreign affairs chief Federica Mogherini and the commissioner heading EU enlargement talks said the arrests went “against European values”.
At least 24 people were arrested in police raids on leading newspaper Zaman and Samanyolu TV station said to have close links with opposition parties.
Those detained are accused of trying to seize control of the state.
The Zaman newspaper and Samanyolu TV channel both have ties to US-based Islamic cleric Fethullah Gulen, the spiritual leader of the Hizmet movement.
A former ally of Turkish President Recep Tayyip Erdogan, Fethullah Gulen – who lives in self-imposed exile – is accused of running a “parallel state” within Turkey.
In a statement, Federica Mogherini and EU Enlargement Commissioner Johannes Hahn said any move towards EU membership depended on “full respect for the rule of law and fundamental rights”.
The raids and arrests “are incompatible with the freedom of media, which is a core principle of democracy,” the pair said in a statement.
“We expect that the principle of presumption of innocence will prevail and recall the inalienable right for an independent and transparent investigation.”
The raids come days after Recep Tayyip Erdogan pledged a fresh campaign against Fethullah Gulen’s supporters.
Journalists, producers, scriptwriters and an eastern Turkey police chief were all arrested, among them the editor-in-chief of Zaman newspaper and the chairman of Samanyolu TV.
Staff at Zaman reported on the incident as police mounted a Sunday morning raid on their offices.
Staff and supporters held placards and chanted “free press cannot be silenced” as police raided the building.
Editor-in-chief Ekrem Dumanli smiled and studied police documents before being led through the newspaper’s headquarters to applause from staff crowded onto balconies.
“Let those who have committed a crime be scared. We are not scared,” Ekrem Dumanli said as he was led into a waiting police car, according to Reuters.
The chairman of Samanyolu TV, which also has links to Fethullah Gulen, was detained in a separate raid in Istanbul.
Hidayet Karaca told reporters the operation was “a disgrace for Turkey” before his arrest.
“Sadly in 21st Century Turkey this is the treatment they dish out to a media group with tens of television and radio stations, internet media and magazines,” the English edition of Zaman quoted him as saying.
Kemal Kilicdaroglu, the leader of Turkey’s main opposition party, called the raids “a coup”.
Staff at Zaman had been expecting the raid after details of the swoop were leaked by a Twitter user known as Fuat Avni, who has previously leaked advance details of police operations.
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