The original version would have directed the National Cancer Institute (NCI) to spend $887.8 million on pancreatic cancer research and create a special 13-member advisory panel to direct the efforts.
The NCI objected to the proposed infringement on its peer-review system, and suggested that prioritizing one condition over another poses ethical challenges for disease scientists.
The first concern, shared by some lawmakers, is that federal health research would become a "Disease Olympics," prompting requests from disease advocates of every stripe.
Sen. Tom Coburn (R-Okla.) made this argument in placing a hold on the bill in September — a hold he maintained until this week.
"We can serve patients best by allowing NIH to determine how to allocate its funding and manpower," he wrote to Senate Minority Leader Mitch McConnell (R-Ky.).
"Congress should have no role in micromanaging the agency [sic] how to perform its research."
On Thursday, Coburn argued that the bill would delay the progress of pancreatic cancer research, but allowed it to pass on a voice vote.
The Senate version, sponsored by Sen. Sheldon Whitehouse (D-R.I.), had 18 GOP co-sponsors.
"The strong, bipartisan vote for this provision is a reflection of the devastating impact these diseases have on families across the country," Whitehouse said in a statement. "I hope it might also signal a brighter future for recalcitrant cancer patients and their families. I am grateful for the support of my colleagues."
The White House has threatened to veto the defense bill over the Senate's departures from the Pentagon’s 2013 budget request and provisions limiting transfers of detainees from Guantánamo Bay.
Final votes are expected Thursday night or Friday.
—This post was updated at 6:11 p.m.