"Interior Minister Gordana Jankuloska, Transport Minister Mile Janakieski as well as the director of DBK Saso Mijalkov presented their resignations," a government spokesman told AFP yesterday. "Prime Minister Nikola Gruevski accepted their resignations."
Spokesman Aleksandar Gjeorgiev did not elaborate on the reasons for their move, which comes after the Balkan nation was rocked by two days of clashes in a northern town at the weekend that left 22 people dead, including eight police officers.
Intelligence chief Mijalkov's resignation letter, published by state-run news agency MIA, said his move was "in the interest of Macedonia" and "would help the political crisis to be resolved." He claimed the crisis was "imposed by the opposition."
The incidents in Kumanovo were the worst in Macedonia for 14 years, and raised fears of fresh unrest similar to the country's 2001 ethnic conflict.
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NATO and the EU have called for a return to calm.
Mindful of the past insurgency and multiple wars during the break-up of the former Yugoslavia, EU officials are particularly keen to prevent ethnically-driven violence from resurfacing.
Thirty alleged gunmen have been charged with terror offences after the bloody shootout that erupted on Saturday at dawn when police moved in on the armed group.
Ethnic Albanians make up around one quarter of Macedonia's 2.1 million population.
Prime Minister Gruevski claimed a "particularly dangerous terrorist group" of ethnic Albanians had been planning a major attack in the Balkan country.
The three top officials who resigned yesterday were being accused by the opposition of involvement in a wiretapping scandal.