[5] Serbia lost effective control over most of Kosovo in the aftermath of the 1998–99 conflict, and virtually all of Đakovica's formerly sizeable Serb population fled the province.
[9] Following his appointment, human rights activist Nataša Kandić issued a public letter accusing Stojanović of breaching the Geneva Convention and domestic laws on the protection of citizens during the Kosovo War.
He rejected the accusations, saying, "I have never in my military career breached the Geneva Convention or the domestic norms on the protection of civilians in times of armed conflict."
He added that Kandić's letter erroneously identified him as head of operations for the Priština Corps during the Kosovo War and accused him of issuing orders for which he was not and could not have been responsible.
[10] Stojanović announced in December 2003 that Serbia and Montenegro's VSB would soon be replaced by a new entity called the Military Security Agency (VBA), falling under the authority of the civilian ministry of defence.
[11][12] The agency was criticized by representatives of the Montenegrin government, including retired general Blagoje Grahovac, who raised objections concerning the manner of its creation.
)[16][17][18] The Sandžak Democratic Party (SDP) called on Stojanović to substantiate his claims about extremist groups in their area,[19] and party leader Rasim Ljajić accused Stojanović of "sull[ying] the reputation of an entire region" by not providing specific information about the alleged terrorist groups.
[27] In October 2007, he charged that the Albanian National Army paramilitary organization was active in Kosovo, Montenegro, western Macedonia, and Albania.
[28] He also said that Albanian paramilitaries were planning for a possible attack on the predominantly Serb community of northern Kosovska Mitrovica in the event that Kosovo did not attain independence via diplomatic means.
[30][31] The election did not produce a clear winner, but the SPS ultimately joined a coalition government with the Democratic Party (DS) and G17 Plus, and Stojanović served as a supporter of the administration.
[34] The Progressives and Socialists formed a coalition government after the election, and Stojanović served as part of its parliamentary majority.
[35] During this time, he urged passage of a law to ban the participation of Serbian nationals as volunteers or mercenaries in international conflicts.
Stojanović responded that the charge was obviously political, made in retaliation against a United Nations decision to form a court to adjudicate war crimes by the Kosovo Liberation Army (KLA).
[45] He later described the charge against him as "totally ridiculous" and said, "in Kosovo today it is possible to bribe any false witness to testify against any member of the Serbian army or police.
Stojanović said he was in favour of a referendum for the final status of Kosovo, adding that the Serbian media would first need to be freed to allow voters to properly understand the situation.
[56] In an October 2024 interview with Danas, Stojanović said that joining the SNS was the greatest mistake of his life, as the party had undermined Serbia's institutions and robbed the country of democracy and freedom during its time in power.
While he credited the SNS's first leader Tomislav Nikolić with initially appointing competent people to oversee the party's regional bodies, he accused Nikolić's successor Aleksandar Vučić of appointing "extremely low-quality people, based on the principle of loyalty," resulting in the entire SNS organization being dominated by "servile, incompetent and blindly loyal cadres."