Oly Ilunga's resignation potentially paves the way for the introduction of a second vaccine to contain the spreading epidemic.

Ilunga has overseen the Congo's near year-long response to what is the second deadliest Ebola outbreak in history.

It has killed more than 1700 and been declared an international health emergency by the World Health Organisation.

President Felix Tshisekedi on Saturday appointed a team led by Jean-Jacques Muyembe, the head of Congo's biomedical research institute, to co-ordinate the government's response in Ilunga's place.

In his resignation letter, the minister criticised pressure by unnamed "actors" to deploy the second vaccine, manufactured by Johnson & Johnson and backed by the WHO.

It has yet to be used on the ground due to Ilunga's objections. It is designed to complement a Merck treatment that has been given to 170,000 people and proved effective.

Ilunga has said the J&J vaccine has not been proved effective and that deploying a second one would confuse people in eastern Congo, where health workers are struggling to overcome widespread misinformation about the haemorrhagic fever, as well as sporadic hostility.

Ilunga said it would be "fanciful to think that the new vaccine proposed by actors who have shown an obvious lack of ethics by voluntarily hiding important information from medical authorities, could have a significant impact on the control of the current outbreak".

J&J says the vaccine has been tested on more than 6000 volunteers and raised no particular safety concerns.

Its chief scientific officer Paul Stoffels said in a telephone interview that the company had been "very transparent, very open and in full communication" with Congolese authorities.

The WHO and other international donors including medical charity Medecins Sans Frontieres have publicly supported using the second vaccine, of which 1.5 million doses are available.

Australian Associated Press