Professor Ian Wilmut said that the "great benefits" made it "immoral" not to carry out therapeutic cloning, the BBC reported Wednesday.
He said the technique could help eradicate inherited disorders.
But the Church of Scotland described his comments as "very naive" and "highly irresponsible."
Last week South Korean scientists said they had cloned 30 human embryos to obtain stem cell lines they hope could one day be used to treat disease.
Professor Wilmut, of Edinburgh's Roslin Institute, said he remained "implacably opposed" to reproductive cloning.
However, he said: "I do envisage that producing cloned babies would be desirable under certain circumstances, such as preventing genetic disease."
He advocated a complex procedure for couples who did not want to pass a genetic disease on to their children.