The Turkish Defence Ministry says four Greek F-16 jets approached Cesme research vessel, with one dropping a chaff flare two nautical miles away from the vessel.
Turkey has said that four Greek jets harassed a Turkish research vessel in the Aegean Sea but Athens denied the accusation, which comes as the two NATO members seek to resume talks over maritime disputes.
One of the Greek fighter jets approaching the TCG Cesme vessel in the west of Lemnos Island launched a chaff cartridge from two nautical miles (2.3 miles) away, according to security sources.
The TCG Cesme was engaged in hydrographic surveying activities during the incident and is slated to continue its scientific and technical research in the region until March 2 under its annual activity schedule.
Defence Minister Hulusi Akar said Turkey responded with the "necessary retaliation...in line with the rules".
"While we are carrying out scientific work, harassment is not appropriate, it is not befitting of good neighbourly ties," he told reporters in parliament.
Chaff prevention systems are found in most military aircraft and are used to trick heat and radar-guided missiles. The cartridges are launched either by the pilots or automatically by on-board systems.
Commenting on the incident, Akar said it was another case of "frequent harassment by our Greek neighbours."
"Our attitude, decision, and efforts we will make on this issue are clear. Nobody should doubt that," Akar added.
The Greek defence ministry said its air-force was conducting a military exercise some distance from the Turkish vessel and denied any harassment.
"No Greek fighter jets flew near the Turkish vessel," Greek defence ministry said.
After a five-year hiatus, Turkish and Greek officials met on January 25 to discuss a decades-old dispute over the delimitation of maritime zones and rights to energy resources in the eastern Mediterranean. The allies have agreed to meet again in Athens, but Greece has continued to escalate tensions.
Since the talks began, formerly known as 'exploratory talks', 20 Greek vessels and numerous air elements have carried out military exercises in the area, including in international waters northwest of Skyros island.
Greece also issued notices of submarine activities on February 10-17, announcing that the islands of Bozbaba (Agios Efstratios), Samothrace, Limnos, Thasos, Lesbos, Chios, Psara, Ahikeria, and Samos islands, which hold demilitarised status, as being within its territorial waters.
It further issued a notice that its submarines would hold a practice-fire exercise in the Aegean Sea and the Mediterranean between March 17 and April 27, again declaring Bozbaba, Samothrace, Limnos, Lesbos, Chios, Psara, as well as the also demilitarised-status Meis, as being within its territorial waters.
Security experts have described Greece's activities as a clear indication of stoking tensions and aversion to compromise, negotiations, and dialogue.
Athens said it has sent an invitation to Ankara suggesting the talks resume in early March, ahead of an EU summit. Ankara has said it wants to continue talks and improve ties with the EU, which backs Greece in the dispute.