Nearly 30 years after the end of its civil war, Bosnia remains fractured along ethnic lines, with NATO troops and later European peacekeepers stationed in the country to help keep the peace.
"We are concerned by secessionist and divisive rhetoric as well as malign foreign interference including from Russia," Stoltenberg told reporters in the Bosnian capital Sarajevo during the first stop of a multi-city tour through the Balkans.
"This threatens to undermine the stability and hampers reform."
The comments came just days after Ukrainian President Volodymyr Zelensky offered a more direct warning, saying Russia was looking to instigate new crises in the Balkans and Moldova to divert the world's attention from the war in Ukraine.
"Pay attention to the Balkans. Believe me, we are receiving information: Russia has a long plan," said Zelensky, according to Ukrainian media.
"If the countries of the world do nothing now, there will be such an explosion again."
Moscow maintains strong links throughout the Balkans, thanks in part to shared cultural and religious ties to the region's Slavic communities.
Bosnia's Serb leader Milorad Dodik remains a key ally of Russian President Vladimir Putin and frequently travels to Moscow.
Dodik is scheduled to appear in a trial this week after being indicted for passing a string of laws that would allow the Bosnian Serb entity to bypass or ignore decisions made by the country's international high representative Christian Schmidt.
Dodik has already hinted that he will not comply with the court's decision if convicted.
The 64-year-old leader has held enormous sway over Bosnia's Serb entity for years and has frequently stoked ethnic tensions with his secessionist threats.
On Monday, Stoltenberg underlined the need for Bosnia's political leaders to work towards unity, reconciliation and strengthening national institutions.
"This is crucial for the stability and the security of the country," he said after meeting Bosnian Prime Minister Bojana Kristo.
Stoltenberg is set to travel to Kosovo later on Monday where he will meet its leaders and visit a NATO camp, followed by trips to Serbia and North Macedonia.
Since the 1992-1995 war Bosnia has remained split into two semi-autonomous blocs -- the Serbs' Republika Srpska and the Muslim-Croat Federation.
The two are linked by weak central institutions.
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