The most dangerous moment in the cold war between Serbia and Montenegro came with the 1999 Kosovo war and its aftermath. The Montenegrin government had declared itself to be neutral in the conflict. It had also given sanctuary to some 40,000 Kosovo Albanian refugees. This put Montenegro on the side of the West against Milosevic's Serbia.

Tensions in the country ran high. Supported by western governments, the Montenegrin authorities build up their police forces. Estimates put the number of Montenegrin police at 10,000-15,000 police, including up to 1,500 well-equipped special police.

They faced the Yugoslav army stationed on Montenegrin territory: 7,000 troops, mostly conscripts but including some 1,100 men of the 7^th military police battalion. President Djukanovic described these in March 2000 as a paramilitary unit loyal to Milosevic "to overthrow the government." Yugoslav army troops conducted house-to-house searches and threatened political allies of Djukanovic. A series of smaller incidents happened through 1999 and 2000:

"On the night of 8-9 December 1999, the Yugoslav Army seized the civilian part of Podgorica airport, after Montenegro had declared it to be Montenegrin government property and had started to build hangars for police helicopters. … On 24 February, a Yugoslav Army checkpoint was established on the Albanian border at Bozaj, after Montenegro opened a border crossing without consulting the federal authorities. On 7 March, a grenade exploded at the police station in Bijelo Polje at the same time as two off-duty members of the VJ 7^th battalion were driving past. … In May 2000, General Milorad Obradovic, the commander of the 2^nd Army (based in Montenegro), issued an order warning that the Yugoslav Army would act decisively against ‘separatist, certain opposition and other enemy forces' which together with foreign enemies were seeking to destroy Yugoslavia."

(ESI Report, 2000)