The Greek ambassador to Albania has been summoned by Tirana, following an incident in which an ethnic Greek man was shot dead by police on Albanian soil.
The incident led to clashes, and is the latest event to rock ties between the neighbours.
Eleni Surani was called in on Wednesday after several days of demonstrations and unrest in Athens and Thessaloniki over the killing, including the firebombing of an Albanian tourism office.
Tirana asked the Greek authorities to "condemn these acts which harm the climate of good neighbourly relations between the two countries," Albania's foreign ministry said in a statement.
Konstantinos Katsifas, who holds both Albanian and Greek citizenship, was killed on Sunday in a shootout with Albanian police in the southern village of Bularat.
Bularat lies on the Albanian side of the border and is home to an ethnic Greek minority.
According to Albanian authorities, police sought Mr Katsifas after he fired a Kalashnikov in the air during a ceremony commemorating Greek soldiers who fought in World War II.
The 35-year-old refused to surrender and fired on police, leading to a 30-minute shootout. A video of Mr Katsifas firing the automatic weapon in the village was broadcast by Albanian media.
Athens has called for more information about the incident, while Tirana has said a thorough investigation is underway.
Albania and Greece have a number of diplomatic disputes, with the treatment of minorities a common source of tension.
The neighbours are also in negotiations due to a long-standing disagreement over their maritime borders.