The article claimed Turkey's President Recep Tayyip Erdoğan ordered Turkish navy to sink a Greek warship without causing any casualties.
Foreign Ministry spokesman Hami Aksoy said the accusations of the Greek government against Turkey in the article are made up.
He said Greece's new provocative policy in the Eastern Mediterranean is disconnected from reality and incompatible with international law.
He urged Greek authorities to put an end to policies that escalate tensions in the Eastern Mediterranean where Turkey is conducting energy exploration within its rights.
Greece has attempted to illegally restrict Turkey’s maritime territory, trying to box it into its shores based on small Greek islands near the Turkish coast.
Turkey has argued the sides should instead sit down for dialogue to reach a win-win solution based on fair sharing.
Greece has also recently carried out military drills - including with France - meant to intimidate Turkey into stopping energy exploration, as well as illegally armed Aegean islands, in violation of longstanding peace treaties.
Athens’ recent maritime delimitation agreement with Egypt also violates Turkey’s continental shelf and maritime rights, sparking further tensions between the two neighbors.