Karadzic is suspected of crimes against humanity
Following a massive operation on Thursday, the Nato-led stabilisation force (S-For) sealed off the area around Celibici, near Foca, for a second time on Friday morning, but it came up empty-handed.
"As a result of extra intelligence we received following [Thursday's] raid, S-For conducted another raid near the town of Celebici in an effort to seize Radovan Karadzic. He was not seized," Nato spokesman Mark Laity told BBC News Online.
The BBC's Defence Correspondent Jonathan Marcus says that the two consecutive operations send a powerful signal to Mr Karadzic and other indicted war criminals still on the run that Nato's waiting game is over.
A statement issued from the alliance's headquarters in Brussels calls upon Mr Karadzic to surrender himself before he is forcibly detained.
Our correspondent says that all the signs are that something has changed within Nato, which now shows a new determination to seize individuals like Mr Karadzic.
Massive operations
The operations are Nato's most visible and large-scale attempts to detain Mr Karadzic.
A report by Reuters news agency said that during the operation German S-For soldiers had blocked roads to Celebici.
Reporters quoted local residents as saying that several helicopters and armoured personnel carriers had been seen in the area.
Mr Karadzic is known to have stayed regularly in the Foca region during his six years on the run from the international war crimes tribunal.
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The charges
Local media reports said hundreds of troops, armoured vehicles and helicopters had been involved in Thursday's operation.
"I think this emphasises our determination to detain all people indicted for war crimes, especially Radovan Karadzic," Mr Laity said.
"The best thing he can do is surrender before he is forcibly apprehended," he added.
Nato Secretary-General George Robertson indicated that Nato would continue its efforts to apprehend Mr Karadzic and other indicted war criminals.
"You can expect more high-profile and low-profile operations until the day comes that those who have been indicted for war crimes... will face justice at the tribunal in The Hague," Mr Robertson said.
"The net is closing in on him and others. There is no way of escape and there is no place to hide," he said.
Karadzic's stronghold
The area around Foca, which lies near the border with Mr Karadzic's homeland of Montenegro, is widely thought to be one of his regular hide-outs.
The region is mountainous and inhospitable and makes the arrest operation particularly difficult.
There is also deep-rooted popular support for Mr Karadzic, who is seen by many there as a war hero, despite attempts by his former political party to distance itself from him.
Bosnian Serb political leaders condemned Thursday's attempt to arrest him, saying they should have been informed.
The Bosnian Serb authorities have yet to arrest a single war crimes suspect.
Mr Karadzic, along with his military commander, General Ratko Mladic, is wanted by the international war crimes tribunal in The Hague on charges including genocide and crimes against humanity.
Recent reports say General Mladic has been seen in the Yugoslav capital, Belgrade.