This blog post reviews a presentation by Jae Brodowsky, a statistician with the U.S. Food and Drug Administration that put to bed the rumor that FDA will only accept submissions where the data analysis was done by SAS. The summary does mention that FDA has certain regulatory requirements for R (or any other statistical package, including SAS).
Smith D. FDA: R OK for drug trials. R-bloggers. Available at: http://www.r-bloggers.com/fda-r-ok-for-drug-trials/