WASHINGTON – The Food and Drug Administration has agreed to work toward faster, more predictable reviews of new prescription drugs in return for millions of dollars in additional fees from drugmakers, under a draft agreement unveiled by the agency on Thursday.

A spokeswoman for the agency confirmed that the new agreement would raise fees about 6 percent, collecting an estimated $40.4 million in new revenue for fiscal year 2012.

The deal comes after months of closed-door meetings between FDA and drug industry officials working to extend a two-decade old program that supplements the agency’s budget with company funding. The latest agreement would require the FDA to provide more meetings and updates on the status of certain drug reviews.

“We’re starting to see a lot of innovative therapies come through as a result of all the investments in science over the last 30 years,” said Dr. Janet Woodcock, director of the FDA’s device center. “So this agreement will continue the review program that allows those products to move expeditiously through the regulatory process so they can reach the public in a timely way.”

Some of the new revenue will also be invested in computers and technology for research, as well as a system for tracking reports of drug side effects. Currently the FDA tracks about 60 million patients across the U.S. through its Sentinel program, but agency officials say the network will need to be much larger to spot emerging drug safety risks.

The deal must be approved and drafted into law by Congress before it expires on Oct. 1 2012. Lawmakers already have granted three 5-year extensions to the program. Since it passed in 1992, the Prescription Drug User Fee Act has allowed the FDA to hire hundreds of additional scientists in return for meeting performance goals.

Last fiscal year, the FDA collected $573 million in user fees under the program, making up 62 percent of its total budget for prescription drug reviews. The portion of FDA’s budget underwritten by industry has steadily increased since 1992, drawing criticism from consumer advocates that the agency has become financially dependent on the companies it regulates. Ten years ago the industry contributed about 49 percent of FDA’s drug review budget.

Woodcock pointed out that some countries rely on user fees for 100 percent of their drug review budgets.

The Biotechnology Industry Organization endorsed the plan in a statement Thursday but stressed that Congress should continue funding the FDA at current levels.