``A good end doesn't make good an action that in itself is bad,'' the Vatican's Pontifical Academy for Life wrote.
The Roman Catholic church teaches that life begins at conception and must be safeguarded from that point. Removing cells from an embryo would kill the embryo, the academy said.
It ``is a gravely immoral, and thus gravely illicit, act,'' the document said.
The academy went on to say that ``every type of therapeutic cloning, which implies the production of human embryos and the subsequent destruction of the embryo products, to obtain stem cells is illicit.''
The academy did not dispute the hope that stem cell research offers and it encouraged the use of cells from adults instead of embryos, which it called ``the more reasonable and humane step.''
``Is it morally legitimate to produce and/or use living human embryos for the preparation'' of stem cells, the academy asked.
``The answer is negative,'' it said.
The Vatican document comes a day after Clinton praised new federal guidelines in Washington allowing research on cells from human embryos. He said the research offered ``potentially staggering benefits'' for those suffering from diabetes, spinal cord injuries, Parkinson's disease and other problems.
The guidelines are vehemently opposed by anti-abortion groups.
In the United States, the National Conference of Catholic Bishops and evangelical Protestant organizations also criticized the guidelines.
"For the first time in history, our federal government will promote research in which developing human beings are destroyed," said Richard Doerflinger, associate director of the bishops' conference's Pro-Life Secretariat. "It is always wrong to directly destroy one innocent member of the human family to help another...We will explore all avenues in Congress and elsewhere for reversing these indefensible guidelines, so medical research may again be guided by sound moral principles."
Some opponents point out recent findings about adult stem cells that may prevent the need for using embryonic stem cells.
"These experiments are unnecessary since research proves that comparable or better results can be obtained from adult stem cells," said William Saunders, senior fellow in human life studies at the evangelical Family Research Council.
Judie Brown, president of the American Life League in Stafford, Va., condemned the guidelines as "false science" that is unneeded. "These guidelines do not present a step forward," she said. "They are an attack against the humanity of the individual human person."
In a statement announcing the publishing of the guidelines, the National Institutes of Health said the guidelines will help ensure that the research is done in a legal and ethical manner. It said the work could result in possible cures and new treatments for diseases such as diabetes, multiple sclerosis and Parkinson's disease.
"The NIH believes the potential medical benefits of human pluripotent stem cell technology are compelling and worthy of pursuit in accordance with appropriate ethical standards," it stated.
The Vatican academy, whose members include both Roman Catholic and non-Catholic scientists, was set up by Pope John Paul II 1994 to help the Vatican understand biomedical issues entwined with ethics.
The pope himself might soon speak out about stem cell research. The Vatican said Thursday he will address scientific conference in Rome next week on transplant advances, including cloning possibilities.
The Vatican is often quick to weigh in on scientific issues which carry ethical implications. Just last week, its official newspaper condemned Britain's move toward easing a ban on human cloning.