NATO-led peacekeepers have "tied and savagely beat up grievly wounded priest Jeremija (Starovlah) and his son with rifle butts, boots and everything that they could," said a letter by Serbian Orthodox Patriarch Pavle to the peackeepers' US commander.
"You are familiar with those facts," the letter to US General Virgil Packett, a copy of which was obtained by AFP, said.
Bosnian Serbs authorities and clergy have already hinted that NATO troops beat up the priest and his son during the raid but NATO strongly denied the allegations.
According to the NATO-led Stabilisation Force (SFOR), the two were wounded when the troops used explosives to blast their way into the priest's house near a church in Thursday's raid in Karadzic's wartime stronghold of Pale, near Sarajevo.
he priest and his 28-year-old son Aleksandar were still in a coma and on life-support machines on Tuesday.
The raid involving some 40 US and British troops followed credible NATO intelligence that Karadzic, charged in 1995 by the UN court for atrocities during Bosnia's 1992-95 war, was hiding in the priest's house.
It was SFOR's third failed attempt to nab Karadzic in Bosnia since he went into hiding after the war.
The UN court's chief prosecutor Carla Del Ponte has repeatedly accused the Bosnian Serb authorities and some members of the Serb Orthodox church in both Serb-run parts of Bosnia and neighbouring Serbia-Montenegro of helping Karadzic evade arrest.
However, Patriarch Pavle assured that "Serbian priests do now hide those charged for war crimes."
The Orthodox Church in Bosnia is part of the Belgrade-based Serbian Orthodox Church.