Metropolitan Amfilohije on Wednesday accused the Montenegrin authorities of "crucifying and persecuting" his Church and of wanting to "grab Church property".
At a service in Cetinje, Bishop Amfilohije said Montenegro was also trying to obstruct the legal residence of his clergy.
Prime Minister Djukanovic on Wednesday revealed that the security services had information that opponents of Montenegrin independence planned to murder the leading Serbian cleric in the country - a passionate oponent of independence - to discredit the independence cause.
Velibor Dzomic, the top Serbian Orthodox priest in Podgorica and the secretary of the church in Montenegro, left the country on Sunday evening after his fourth application for a residency permit was turned down by the Ministry of Internal Affairs.
Kosovo's Foreign Minister, Hashim Thaci, is due to visit Podgorica for a two-day visit on Thursday when he will meet the country's top officials.
However, the visit of the former leader of the Kosovo Liberation Army remains controversial among Montenegrins who cherish ties to Serbia.