The companies will have to divest assets needed to make 11 generic injectable drugs as a condition of approving the deal, the FTC said.
The deal for Agila, which is based in Bangalore, was valued at $1.6 billion when it was announced in February.
The purchase is expected to help Mylan, one of the world's largest generic drugmakers, double its injectable drugs portfolio.
The assets that are to be divested are: anti-arrhythmic heart drug amiodarone hydrochloride; surgical anesthetic etomidate injection; cancer drug fluorouracil; hypertension drug labetalol hydrochloride; detoxifying agent mesna; pediatric cancer drug methotrexate sodium (preservative-free); acetylcysteine injection, used to minimize liver damage following an acetaminophen overdose; fomepizole injection, used to treat some types of accidental poisoning; antiviral herpes drug ganciclovir; last-resort antibiotic meropenem.
Assets related to the transplant drug mycophenolate mofetil, which is currently only a branded drug but which is expected to have generic release in the near future, also must be sold.