The regulator launched a review of the drugs in September in light of some rare cases of severe liver injury among patients.
It said on Thursday that the drugs were beneficial in the treatment of obese or overweight patients with a body mass index (BMI) of 28 or above.
However, it recommended that labeling for the medicines, including nationally authorized orlistat-containing generics, was harmonized to ensure the warning about liver damage was consistent.
It stressed that cases of severe liver disease linked to the drugs were very rare.
There with 21 cases of severe liver toxicity reported where Xenical was considered a possible cause from 1997 to January 2011, it said, and nine reports of liver failure in people using Alli between May 2007, when it was first marketed, and January 2011.
To put that in context, Xenical and Alli together were estimated to have been used by over 53 million people worldwide, with over 20 million in the European Union, it said.
GlaxoSmithKline has put Alli up for sale as part of a disposal of non-core brands.
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