Brother Manuel Garcia Viejo, 69, director of a hospital in the Sierra Leonean town of Lunsar, "has tested positive (for Ebola) and has expressed his desire to be transferred to Spain", the health ministry said in a statement released on Saturday.
In a serious condition, he is already being treated at Madrid's Carlos III hospital, Spain's 20 minutos newspaper reported.
However, the hospital's director José Ramón Arribas on Monday said Viejo would not be treated with ZMapp as there were no more supplies of the drug.
Viejo is the second Spaniard to contract Ebola in the current outbreak.
The health ministry said the risk to public health in Spain from the patient was "practically nil".
Garcia is a member of the Hospital Order of San Juan de Dios, a Roman Catholic group that runs Juan Ciudad, a charity working with Ebola victims.
On Saturday he was being treated in an Ebola unit in the Sierra Leone capital Freetown, the order said in a statement.
Garcia, a specialist in internal medicine, is also qualified in tropical medicine. He has worked in Africa for 30 years and has been director of the hospital in Lunsar for the past 12 years, it said.
Sierra Leone on Saturday began the second day of a 72-hour nationwide shutdown aimed at containing the spread of the deadly virus.
Most of the country's six million people were confined to their homes from midnight (0000 GMT) on Friday, with only essential workers such as health professionals and security forces exempt.
Spanish health officials did not expect the curfew to impede their efforts to fly Garcia out of the country, however.
The ministry said late Saturday that his repatriation would take place "in the coming hours" and he would be taken straight to Madrid's La Paz-Carlos III hospital.
In August a 75-year-old Spanish priest became the first European to die from Ebola during the current outbreak in west Africa, the worst since the disease was first discovered four decades ago.
That missionary, Miguel Pajares, was infected in Liberia, where he worked with Ebola patients.
The epidemic has so far killed more than 2,600 people in west Africa, the UN World Health Organization said Thursday.
No vaccine or medicine is available for treating Ebola. Pajares was treated with an experimental US serum, ZMapp, while in isolation in La Paz-Carlos III.
The virus causes severe muscle pain, vomiting, diarrhoea and -- in some cases -- unstoppable internal and external bleeding.
British nurse William Pooley, 29, who was infected with Ebola while working in Sierra Leone, recovered this month following treatment with ZMapp.
France on Friday authorized "experimental treatments" for a French nurse with Ebola who was flown back from Liberia.