Rodriguez received a therapeutic use exemption for the otherwise-banned substance clomid, according to the book "Blood Sport: Alex Rodriguez, Biogenesis and the Quest to End Baseball's Steroid Era," which was published last week.
Clomid is prescribed for ovulation induction and has been used by men to restore the production of testosterone following a steroids cycle. The book said the exemption was granted by Bryan W. Smith, then the independent administrator of baseball's drug program.
"We did not know about it at the time," Selig said Tuesday before the All-Star game during the commissioner's annual meeting with the Baseball Writers' Association of America. "These independent people made a judgment. History proved them I guess it turned out to be somewhat wrong, but they were outstanding doctors."
Rodriguez admitted in 2009 that he used a banned performance-enhancing substance while with the Texas Rangers from 2001-03.
The New York Yankees third baseman is serving a season-long ban this year after an MLB drug investigation; an arbitrator ruling on the discipline concluded there was "clear and convincing evidence" Rodriguez had used three banned substances.
Smith was the program's administrator from 2006 until he was replaced in June 2012 by Dr. Jeffrey M. Anderson.
"I probably shouldn't say this," Selig revealed, "the administrator at that time later was let go because he was too tough, as I remember."