WASHINGTON (Reuters) - The U.S. Senate on Thursday showed near-unanimous support for a bill that helps fund the U.S. Food and Drug Administration, a regulatory powerhouse with sweeping influence over the foods Americans eat and the medicines they take.

The bill, which passed by a vote of 96 to 1, aims to speed approval of new drugs and devices and ensure food safety. It reauthorizes fees from companies like Johnson & Johnson, Medtronic Inc and Roche Holding AG that help speed FDA evaluation of new medical products prior to approval.

These so-called user fees could provide almost half of the FDA's proposed $4.5 billion budget for next year. The FDA regulates products that make up about a quarter of the U.S. economy.

The Senate's approval caps a more than year-long process to find common ground among the FDA, industry and patient groups, with a focus on medical device regulation. Medical device makers had at first balked at higher fees, accusing the FDA of slow and inconsistent reviews.

The device industry and the FDA finally agreed on fees in February, about a month past their deadline. At the same time, patient groups called for stricter device regulation to protect safety, and said the current bill does not go far enough.

Similar legislation has passed a U.S. House of Representatives committee with bipartisan support and may move to the full House for a vote as early as next week.

In a rare show of cooperation between Democrats and Republicans, Senate leaders sped the bill through the Democratic-controlled chamber, emphasizing its importance in protecting consumer safety and promoting innovation in medicine.

This bill is a shining example of what we can achieve when we all work together, said U.S. Sen. Tom Harkin, an Iowa Democrat and chairman of the Senate committee that oversees the FDA.

Industry user fees, first enacted in 1992, give the FDA millions of dollars annually to review new products for the U.S. market but must be renewed every five years. The current version is set to expire in September.

Starting this year, for the first time the FDA will also collect fees from makers of generic drugs and of copycat versions of complex biotech drugs, known as biosimilars.

DRUG SHORTAGES

The bill would also force drug companies to tell the FDA about looming shortages, which have hit the supply of critical cancer, antibiotic and nutrition drugs.

The number of scarce drugs escalated to 250 last year, from 56 in 2006 - but the FDA has said it was able to prevent 128 drug shortages in six months after getting earlier notification from companies.

I'm glad we were finally able to give the FDA the tools it needs to prevent shortages, said Sen. Amy Klobuchar, a Minnesota Democrat who was the first to propose the drug shortages legislation last year, along with Robert Casey, a Democrat from Pennsylvania.

But she emphasized early notification was only a first step in trying to solve the problem of drug scarcity.

The bill also gives the FDA new authority, such as speeding approval for drugs that show early promise, and gives drugmakers incentives to invest in antibiotics for life-threatening conditions.

But some criticized the bill for not doing enough for patient safety.

Consumers Union, an advocacy group that has lobbied for changes to U.S. medical device regulation, said the bill should have prohibited the FDA from approving new devices based on faulty predecessors, and should have established a national registry to track problems with devices like hip implants or surgical mesh.

Congress is missing the opportunity to fix a broken system that lets too many unsafe medical devices on the market, said Lisa McGiffert, director of the Safe Patient Project at Consumers Union.

(Additional reporting by Donna Smith in Washington; editing by Carol Bishopric and Matthew Lewis)