The new guidelines classify gene therapy, somatic cell therapy and tissue engineering as medical procedures, make all medicines involved in such treatments subject to a scientific safety evaluation, and provide for post-treatment monitoring of patients.
Evaluation will be carried out by a special committee at the London-based European Medicines Agency.
In adopting the new rules, EU environment ministers stopped short of an EU-wide ban on treatments based on stem cell research as demanded by some Catholic countries.
Nevertheless, individual EU nations are still free to reject specific types of treatments or medicines based on genes, cells and tissues on ethical grounds.
The rules were backed by the European Parliament in April, after amendments by Catholic lawmakers demanding stem cell research be outlawed were defeated.
The EU funds embryonic human stem cell research from its own budget only under strict conditions that include a ban on research aimed either at human cloning for reproductive purposes or at modifying the genetic makeup of human beings.
Advocates of stem cell therapy say it could lead to cures for many diseases, including diabetes and spinal cord injuries. Opponents says its not ethical.
Embryonic stem cells have the ability to become any tissue in the body, and leading scientists see them as a possible source of medical breakthroughs. But the research sometimes involves the destruction of frozen embryos created for in vitro fertilization, a step that stirs passions and debate over the beginning of life.