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Ngeze said at a news conference he was going "to investigate to find out what had become of him" and would reveal his findings in the next few days. The news conference was transmitted on Radio Burundi and rebroadcast on Rwanda radio.
He added that deaths had occurred and he "regretted" that.
Ngeze also said in the radio broadcast that "democratic institutions" would be restored in Burundi if the coup leaders were not prosecuted.
Burundi diplomatic sources said Ngeze should explain the reason for the coup and reveal Ndadaye's fate before forming a government.
Burundi's capital was calm, according to officials of the International Committee of the Red Cross (ICRC) here who said they had contacted colleagues in Bujumbura.
Bujumbura remained under curfew, air and telephone links remained cut and the borders sealed.
The soldiers who reportedly carried out the coup belong to the minority Tutsi tribe, which has traditionally dominated Burundi's executive branch of government and the armed forces.
Comparable Tutsi coups have led to massive bloodlettings, with up to 200,000 Hutus reportedly massacred in 1972 and 20,000 killed by the army in 1988.
Ndadaye became Burundi's first Hutu president in June after winning the country's first multi-party elections.
U.N. Secretary General Boutros Boutros-Ghali condemned the coup at a press conference in Ethiopia Saturday and expressed his "solidarity with the Burundians."
France suspended all military and civilian cooperation with Burundi but humanitarian aid will continue, a foreign ministry statement issued in Paris said.
The European Community was considering what action to take to isolate Burundi politically and economically in order to resolve the crisis, the statement added. On Friday, the E.C. froze all aid to Burundi.
Egypt, Congo and Zaire became the latest states to condemn the coup.
Egypt, which holds the presidency of the Organisation of African States, said it would ask the U.N. Security Council to take steps against the coup leaders.
AFP AFP
