Djukanovic, who has run the small Adriatic country for nearly 30 years, doubled down on the stance as Montenegro is roiled by protests over the status of the Serbian Orthodox Church (SPC) inside its borders.
Long-running tensions over the issue exploded when the government passed a law in December that could turn many of the church's oldest monasteries into Montenegrin state property, trigging huge demonstrations.
The SPC, based in Belgrade, is still the main religious body in Montenegro, which was one country with Serbia for nearly 90 years until 2006.
Speaking to AFP in the Montenegrin capital Podgorica, the president accused SPC clergy of undermining his efforts to consolidate the country's 14-year independence.
"The Serbian Orthodox Church is among important instruments used by the ideologists of a 'Greater Serbia' nationalism against Montenegro, against Montenegrin independence, against its national, cultural and religious identity," Djukanovic said.
The 57-year-old called for the creation of an autonomous branch of the Orthodox church in Montenegro, similar to the Ukraine church's split from Russia.
It would "would unite all Orthodox believers, both those of Serbian and those of Montenegrin national affiliation," explained the leader of a country where around a third of the population identify as Serb.
While an independent Montenegrin church was declared in the early 1990s, its footprint and flock are still tiny, and its religious authority is not recognised by the major Orthodox power centres.
- Prayers and protests -
While Djukanovic's government defends the new property law, the SPC has flexed its muscles over the past month and a half by mobilising tens of thousands of demonstrators to weekly prayer marches across a country of around 620,000 people.
Priests accuse the ruling party of preparing to plunder its holy sites, which include more than 600 monasteries and churches dotting the country's rocky, picturesque landscapes.
Djukanovic, a shrewd politician who masterminded Montenegro's independence, replies that the clergy are "skilfully manipulating" believers.
He insists the churches will remain open for use for the Orthodox faithful, though he doesn't hide his desire to eventually cut off the spiritual chain of command from Belgrade.
For Djukanovic, creating a separate church is the next "logical" step after securing Montenegro's independence.
"We are driven...by an undisputable need to complete the spiritual, state and social infrastructure that will strengthen citizens' awareness of their own identity," he told AFP.
"We do not accept the ideas of 'Serbing' Montenegro," he added.
The church issue has put sensitive identity debates about Serbia and Montenegro's entangled histories at the centre of politics in the run-up to elections later this year.
It has also deepened hostility and dysfunction in parliament, where Djukanovic's ruling DPS party faces a pro-Serb opposition which aligns with the Church.
Some critics accuse Djukanovic of using the religious issue to rile emotions and distract from other problems that have festered under his rule.
Those include low wages, widespread corruption and threats to media freedoms, all of which are standing in the way of Montenegro's dreams to join the European Union, a goal tentatively set for 2025.
Others say Djukanovic's domination of power -- serving as either prime minister or president for most of the past three decades -- is the main obstacle to Montenegro's democratisation.
The president, however, counters that this is the cry of sore losers, encouraging his rivals to work harder if they want to win elections expected in autumn.
"If my opponents expect that I should make a concession to them so they could reach their goal, a victory by handing them power without elections, they are wrong," he said.