Billions of dollars offered by Congress as a lifeline to small businesses struggling to survive the pandemic are about to be left on the table when a key government program stops accepting applications for loans.

Business owners and advocacy groups complain that the money in the Paycheck Protection Program was not fully put to work because the program created obstacles that stopped countless small businesses from applying. For those that did seek loans, the ever-changing application process proved to be an exercise in futility.

“It was a flawed structure to begin with,” said John Arensmeyer, CEO of Small Business Majority, an advocacy group. “It favored established businesses. It was set up to give money to people with strong banking relationships.”

The program’s shortcomings also made it more difficult for minority businesses to get loans, according to a report from the Center for Responsible Lending, a research group.

The loans were designed to give companies devastated by government-ordered shutdowns money to pay staffers and survive. The money was aimed at small businesses such as restaurants, retailers and salons that are desperately trying to stay afloat as the U.S. economy reopens in fits and starts.

As of late Friday, the Small Business Administration had approved more than 4.7 million loans worth nearly $518 billion. Small businesses that also included medical offices, dry cleaners and manufacturers obtained money that ultimately saved jobs and eased the unemployment rate from April’s staggering 14.7 percent to May’s still-excruciating 13.3 percent.

But more than $140 billion in loan money remained unclaimed out of $659 billion allocated by Congress. It will be up to Congress to decide what to do with any leftover funds, an SBA spokeswoman said.

“After overcoming initial problems at launch, the SBA’s Paycheck Protection Program has provided a critical financial lifeline to small businesses across the country. Working in partnership with the federal government, banks of all sizes stepped up to deliver over $500 billion in PPP loans that helped small business customers in need, despite challenges from the ongoing pandemic and changing regulatory guidance. The size, scale and speed of the response was unprecedented,” the American Bankers Association said in a statement. “According to the Treasury Department, the 4.8 million PPP loans supported an estimated 50 million jobs. Unfortunately, there are still too many Americans and too many businesses feeling economic pain from this pandemic. As PPP expires, America’s banks will continue to support their business customers and do their part to spur the economic recovery to come.”