"If such a situation happens, I think and I know that the family of President Bongo would naturally inform me. This is not the case at the moment I am talking to you," Ndong told Gabonese television on Sunday.
Separately, a Spanish diplomatic source also denied reports of Bongo's death.
Bongo was hospitalised in Spain late last month, amid reports that he was ill with cancer.
Miguel Angel Moratinos, Spain's foreign minister, said then that Bongo had been admitted "for medical treatment" at a clinic in Barcelona.
Sources close to the president in Libreville, Gabon's capital, had said only that Bongo had undergone an operation and was "better" following the May procedure.
Bongo ruled the former French colony of Gabon for 41 years, in a reign overshadowed by corruption allegations, which he denied.
Last month, a French judge said that an investigation was under way into Bongo's financial activities in France, as well those of Denis Sassou Nguesso and Teodoro Obiang Nguema, his respective counterparts from Congo-Brazzaville and Equatorial Guinea.
Transparency International, the corruption watchdog, said that the leaders embezzled millions of dollars of public money to fund a lavish lifestyle.
All three leaders denied the claims.