Greek Cypriot leader Tattos Papadopoulos and his Turkish counterpart, Mehmet Ali Talat, spent about an hour in talks in Nicosia, the BBC reported.
It was the first time the two have met in two years after a peace effort collapsed, The Times of London said.
Talat said progress was made on trying to find and return the missing or their remains, and described the mood as "good and sincere," the BBC said.
Cyprus has been divided since Turkey invaded in 1974, in the wake of a failed coup by supporters of union with Greece.
Attempts to resolve the dispute have been stalled since 2004 when Greek Cypriots rejected a peace plan that had been endorsed by Turkish Cypriots. Greek Cypriots have entered the European Union while the Turkish Cypriot region is recognized as a country only by Turkey.