WASHINGTON—When SAC Capital Advisors LP was weighing an investment in Vertex Pharmaceuticals Inc., the hedge-fund firm contacted a source it knew would provide nonpublic information without blinking: the federal government.

An investment manager for an SAC affiliate asked the Food and Drug Administration last December for any "adverse event reports" for Vertex's recently approved cystic-fibrosis drug. Under the Freedom of Information Act, the agency had to hand over the material, which revealed no major problems....