Karadzic had used the name Dragan Dabic during more than 11 years on the run, some of which he spent in Belgrade practicing alternative medicine in a private clinic.
"This man is real, he is alive," the ministry said of Dragan Dabic, giving no further information in its statement.
Serbian media reports on Wednesday said Dabic was killed in Sarajevo, during the 1993 siege of the Bosnian capital, ordered by Karadzic, when thousands were killed. The B92 television channel even quoted Dabic's brother as saying he had been shot by a sniper when he was going for humanitarian aid.
Karadzic moved freely in Belgrade without raising suspicions among the public. When he was arrested he had a bushy white beard and long gray hair and bore little resemblance to his former self. He was even reported to have published articles in the Healthy Life journal.
Karadzic's lawyer said Thursday that contrary to official reports the ex-president was arrested on Friday, not Monday. Svetozar Vujacic said his client was taken to an unknown location and held for three days, adding that the judicial authorities were unaware of the illegal detention.
Vujacic said three witnesses saw his client being detained on a public bus in Belgrade's suburbs. The lawyer said he would lodge a lawsuit against the kidnappers.
The move is seen as an attempt to delay Karadzic's extradition to the UN war crimes tribunal in The Hague.
A judge in Belgrade ruled Tuesday that Karadzic could be tried at The Hague tribunal. And Bruno Vekaric, a spokesman for Serbia's war crimes prosecutor, said his extradition "could take place on Monday or Tuesday - but it could be earlier."