"Karadzic was the main priority of our operation... he was not found," Matthew Brock, an SFOR spokesman, told reporters in Pale.
Following a tip-off that Karadzic, who has eluded international troops for eight years, may be in need of medical attention, NATO-led Stabilisation Force (SFOR) troops arrived in Pale on Saturday and searched clinics and the home of his wife.
Brock said documents and ammunition were taken from Ljiljana Karadzic's home.
"We hope that this particular documentation would lead to success in our future operations," he said without providing any details.
SFOR Captain Dennis Thaagaard, who participated in the search, said evidence was found of Karadzic's contacts with his family.
"We have clear evidence that he had contacted his family and his inner support network," Thaagaard said.
Cat and mouse
Karadzic, 58, along with his military chief Ratko Mladic, has played cat-and-mouse with NATO-led troops since they were dispatched to Bosnia in 1996 to oversee the Dayton peace accord.
He is charged by the UN court with genocide and crimes against humanity during the 1992-95 war, notably for the siege of Sarajevo and the July 1995 massacre of more than 7,000 Bosnian Muslims in Srebrenica, Europe's worst single atrocity since World War II.
Karadzic is still seen as a hero among many in the Republika Srpska, the postwar entity which along with the Muslim-Croat Federation makes up Bosnia.
Over the past two years SFOR has conducted a series of failed operations to track him down.
Italian soldiers stand in front of
Radovan Karadzic's house in Pale
But Karadzic's wife Ljiljana denied she had been in contact with her husband.
"The personal photographs they seized dated from 1992-1997 -- how does that prove that I'm contact with my husband," she told AFP in a telephone interview.
"They searched my house, our cars, even the septic tank - do they think Radovan Karadzic is hiding like some Saddam Hussein," she said in a reference to the Iraqi leader, who was found in by US troops last month in an emptied septic tank.
Karadzic's daughter Sonja fumed at search of the house where she was with her mother and two children.
"I am outraged with SFOR because they are molesting my family and children. They are throwing our photos, documents and jewellery around and don't let us enter rooms that have already been searched," she told AFP.
She added that they had been "practically imprisoned" in the house since Saturday when SFOR surrounded it and she was allowed to leave only once when troops searched her medical practice. She refused to talk about her father.
Operation to end
SFOR said they hoped to reduce the operation on Sunday evening, but would maintain presence at checkpoints set up on all streets leading out of the town.
"SFOR would hope to finish the operation tomorrow (Monday) afternoon," Brock said.
SFOR said they detained one person known to support war crimes fugitives, and Bosnian Serb radio said a second person had been detained later.
Bosnian Serb police, who also took part in the operation, said SFOR also searched during the night the premises of the Se Cross, which Ljiljana Karadzic previously managed.