Cardinal Javier Lozano Barragan of Mexico, who acts as the Vatican health minister, said that stem cells taken from human embryos and involving the destruction of the embryos "serve no purpose".
Asked whether the Vatican was concerned about reports that Mr Obama might reverse the Bush Administration's ban, the cardinal said that embryonic stem cell research had not resulted in any significant health cure so far and was "good for nothing".
Research on adult stem cells and umbliical cords had been shown to have "positive value", by contrast, although even that was not "a panacea for everything."
He said the Vatican would seek clarification of the new administration's position on stem cells, and he himself was not "fully aware" what it was.
Aides to Mr Obama indicated this week that he will reverse Mr Bush's stand on stem cell research. The US Senate voted in July to remove restrictions on embryonic stem cell research, but the President vetoed the legislation the following day.
Mr Obama has supported stem cell research to find cures for diseases such as Alzheimer's. His views are supported by Joe Biden, the Vice-President-elect, who is a Roman Catholic.
John Podesta, who is handling the President-elect's preparations to take over in the White House on January 20, said Mr Obama wanted "all the Bush executive orders reviewed".
He added: "I think across the board, on stem cell research, on a number of areas, you see the Bush administration even today moving aggressively to do things that I think are probably not in the interest of the country."
Writing in the National Catholic Reporter, John Allen, a leading American Vatican watcher, said the Vatican would have "deep differences" with the Obama administration over abortion and embryonic stem cell research.
These, however, must not be allowed to impede US-Vatican co-operation in promoting "religious freedom and human dignity worldwide" or on issues such as immigration, economic justice, peace, and environmental protection, he said.
Carinal Barragan, President of the Pontifical Council for the Pastoral Care of Health Care Workers, made the remarks at a press conference on childhood disease and illness and infant mortality.
He called for an intensive effort to improve "both medical and pastoral" aid to children, saying that four million babies in the world died each year in their first 26 days of life.
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(Source: TO)