Washington Post columnist David Ignatius said Prime Minister Recep Tayyip Erdogan's government had last year revealed to Iranian intelligence the identities of up to 10 Iranians who had been meeting in Turkey with Mossad handlers.
But Turkish Foreign Minister Ahmet Davutoglu said the allegations were "without any foundation".
"(Turkish intelligence chief Hakan) Fidan and other security agents report only to the Turkish government and the parliament," he said.
Relations between Israel and Turkey, once its closest Muslim ally, have deteriorated dramatically since an Israeli raid on a flotilla of aid bound for Gaza in 2010 that left nine Turks dead.