The Turkish pilot was rescued by a merchant ship, while a Greek helicopter and navy vessels searched for the Greek pilot after the two F-16 jets crashed into the sea 20 kilometers (12.5 miles) south of Karpathos, Greek and Turkish authorities said.
Greek officials retracted earlier statements that two pilots had been on board the Turkish plane, which they had initially identified as an R-F4 fighter jet.
Greek and Turkish fighter planes frequently intercept each other over the Aegean, mostly in areas of disputed airspace, the AP reports.
"It appears the incident occurred while the Greek plane was intercepting the Turkish jet," government spokesman Evangelos Antonaros said. "This is a particularly unfortunate incident."
Turkish Defense Minister Vecdi Gonul said his country's chief of staff was in contact with his Greek counterpart over the incident.
Greek Foreign Minister Dora Bakoyannis contacted her Turkish counterpart, Abdullah Gul, following the crash.
"The two ministers expressed their regret for today's incident and agreed that this incident must not affect the two countries' goal of improving their relations," the Greek Foreign Ministry said in a statement.
Greece says its national airspace extends to 10 miles (16 kilometers), but Turkey recognizes only six miles (10 kilometers) - the same distance as territorial waters. Athens often scrambles fighter planes to intercept Turkish jets it claims are violating its airspace - an accusation Ankara rejects.
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