Harkin and Enzi are chairman and ranking member of the Senate Health, Education, Labor and Pensions Committee.
The NCPA added in its letter that drugs to treat ADD and ADHD have seen the worst shortages.
"We believe that these controlled substances are in short supply, in part, because of the inflexibility of the current DEA quota system," the group wrote.
The notice came ahead of looming Senate action on the FDA bill (S. 3187), which has drawn praise for passing smoothly through the legislative process so far.
Congress has until the end of September to reauthorize the user fees that the FDA collects from drug and medical device makers.
The Senate is expected to hold final votes by the end of the week. The House version is ready for a floor vote.
On drug shortages, the Senate bill would develop a task force and order at least one study.
The NCPA recommended that it also include language asking the DEA to move more quickly on manufacturer requests to increase quotas for "certain controlled substances that are in short supply."
Grassley and Whitehouse asked federal investigators to probe the same issue in a May 3 letter.
"The Drug Enforcement Administration has to walk a fine line between managing dangerous controlled substances like painkillers and making sure there are adequate supplies for legitimate medicine," Grassley said in a statement.
"A non-partisan study by a neutral entity is needed to ensure that the proper balance is struck in the best interests of everyone involved,” he said.