The news comes just days after three nurses from the same facility died of the disease, which has killed hundreds of people throughout west Africa and continues to spread.
Dr Omar Khan was in charge of the main Ebola treatment centre in Kenema, around 320 kilometres (200 miles) east of the capital Freetown, when he caught the virus.
Health Minister Miatta Kargbo called Khan a "national hero", praising his "tremendous sacrifice."
"I will do anything and everything in my power to ensure he survives. I call on all Sierra Leoneans to remember him in their thoughts and prayers," he said.
Khan has been transferred to another treatment facility run the medical charity Doctors Without Borders (MSF), the health ministry said.
"He is responding to treatment and is very cheerful and fine," Dr Abubakarr Fofanah, the deputy health minister, told AFP by phone.
The news of Khan's illness came as the health ministry confirmed the deaths of three nurses on Monday, describing them as "veterans who have spent over 15 years working in infectious diseases and have saved the lives of more than 100 people."
"The last few days have been challenging to us at the ministry. These people were a source of hope and inspiration," spokesman Yahya Tunis told journalists on Wednesday.
Nurses at the Kenema Ebola centre, located within a government-run hospital, are now calling for it to be relocated to another site and for MSF to take over the running of the facility, Tunis added.
Amid growing concern over the spread of the virus, activists have launched a campaign urging President Ernest Koroma to cancel an August trip to a US-Africa summit in Washington to deal with the crisis.
"He should cancel the trip and declare the Ebola outbreak a national emergency," said journalist Lamrana Bah, who is leading the campaign.
Ebola is a form of haemorrhagic fever which is deadly in up to 90 percent of cases.
It can fell victims within days, causing severe fever and muscle pain, vomiting and diarrhoea -- and in some cases, organ failure and unstoppable bleeding.
According to the latest figures from the health ministry released on Wednesday, 422 cases of Ebola have been reported in Sierra Leone, leading to 143 deaths.
In addition to Sierra Leone the virus has swept through Guinea and Liberia leaving more than 800 people dead, according to the World Health Organisation.