An Airbus A310 carrying 75-year-old Roman Catholic priest Miguel Pajares landed at the Spanish capital's Torrejon military air base at 8:15 am (local time), the Defence Ministry said in a message on Twitter.
The priest had tested positive for Ebola at the Saint Joseph Hospital in the Liberian capital Monrovia where he worked, according to the Spanish aid organisation that employs him, Juan Ciudad ONGD.
The military flight also evacuated Spanish nun Juliana Bonoha Bohe, who had worked at the same hospital, the ministry said. She is not known to be infected with Ebola but is nevertheless to be isolated for treatment.
Since breaking out earlier this year, the epidemic has claimed 932 lives and infected more than 1,700 people across west Africa, according to the World Health Organization.
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Other cases have been reported in Guinea, Sierra Leone and Nigeria.
Two Americans who worked for Christian aid agencies in Liberia and were infected with Ebola while taking care of patients in Monrovia were brought back to the United States for treatment in recent days.
"This news has lifted my spirits, it is great, I am very happy. It is worth fighting on," the priest told the online edition of daily Spanish newspaper ABC by telephone when informed yesterday that he would be repatriated.
The Spanish priest had been in quarantine at the Saint Joseph Hospital in Monrovia, along with five other missionaries, since the death on Saturday of the hospital's director from Ebola.
Juan Ciudad ONGD, which runs hospitals around the world, has asked the Spanish foreign ministry to fly out the two women.