The Treasury Department is asking publicly traded companies who received loans from a fund intended to help small business recover from the pandemic to return the money by May 7 or face consequences, according to new guidance issued on Thursday.

The department said it was "unlikely that a public company with substantial market value and access to capital markets" could prove that a federal loan was necessary for it to stay afloat.

The request from the Treasury Department came after large companies who took loans from the program were criticized heavily as the fund ran out of money — and many small businesses, which the money was intended to help, were unable to get a loan.

Large companies were able to access the funds through a loophole in the restrictions that was meant to save the loans for small-business use only.

Companies who pay back the loan in full by May 7 will be considered to have made their requests "in good faith," the guidance said.

But, some companies that qualify as small businesses according to the Small Business Administration's guidelines are still publicly traded, said JP Hannan, chief financial officer of Florida-based AutoWeb, which has 83 employees and received $1.4 million of the funds.

Companies like AutoWeb, which trades as AUTO on the Nasdaq, "shouldn't be penalized simply because we have a ticker symbol," he said.

Treasury Secretary Steven Mnuchin said on Tuesday that "there are severe consequences for people who don't attest properly to this certification. And again, we want to make sure this money is available to small businesses that need it, people who have invested their entire life savings."

Some companies, like Shake Shack, which received a $10 million loan, said the process was confusing, and when they realized small businesses couldn't access the fund, they gave back their loan to free up more cash. But, some businesses, such as Potbelly, have held on to their money.

Ruth's Chris Steak House, which kept the loan after Shake Shack and others returned the funds, said on Thursday that it would return the money after the request from the Treasury Department. In a statement to Business Insider, the company said, "We intended to repay this loan in adherence with government guidelines. As we learned more about the funding limitations of the program and the unintended impact, we have decided to accelerate that repayment."