On April 2, the CEO of Windtree Therapeutics, a biotech and medical-device company, boasted of “tremendous progress” the company made in 2019, capped by a December stock sale that netted the Bucks County firm $23 million.

“Our strengthened balance sheet allows us to focus on our multiple clinical development programs,” chief executive Craig Fraser said in a statement announcing the company’s fourth-quarter financial results.

Just a week later, Windtree applied for an emergency small-business relief loan available as part of the sweeping coronavirus economic rescue package. On April 20, the Warrington-based company, which employs 32 people, won approval for a $546,600 loan, regulatory filings show.

Windtree was among at least 20 publicly traded companies in Pennsylvania and New Jersey that won approval for at least $48.6 million in government-backed loans under the troubled Paycheck Protection Program (PPP), according to an Inquirer analysis of records filed with the Securities and Exchange Commission.

Some Philadelphia-area companies that received loans were struggling to turn a profit long before the coronavirus pandemic sent the economy into a free fall, records show, and one was already warning investors that it might need to file for bankruptcy. Others had access to capital as part of existing agreements with banks, raising questions about whether they needed federally backed loans to continue their operations.

PPP was intended to help small businesses with up to 500 workers keep employees on the payroll while states shut down wide swaths of economic activity to mitigate the spread of the coronavirus. The loans are forgivable if recipients meet certain conditions, such as spending most of the money on payroll, rent, and utilities. Congress initially authorized $349 billion for the program, and lawmakers allocated an additional $310 billion after the initial funding quickly ran out.

But it has come under scrutiny in recent weeks as large companies such as the burger chain Shake Shack and the NBA franchise Los Angeles Lakers disclosed that they had received loans, even as mom-and-pop shops struggled to get banks to take their applications. Nationally, almost 300 public companies received $1 billion in PPP loans, the Washington Post reported.

Trump administration officials last week warned big companies not to exploit the program. Treasury Secretary Steven Mnuchin said they could face “criminal liability."

“The purpose of this program was not social welfare for big business,” Mnuchin said on CNBC.

And the Small Business Administration, which oversees the program, updated its guidance, telling borrowers that “it is unlikely that a public company with substantial market value and access to capital markets” would be eligible.

While companies such as Windtree are not corporate giants, their ability to access millions in capital that aren’t available to small private businesses underscores the challenge of fairly implementing a huge new government program at a time when public officials and bankers were under pressure to distribute the money as quickly as possible.

Facing public backlash, some companies have said they will return the loans. Besides national chains such as Shake Shack, Pennsylvania companies such as Yardley-based Optinose Inc. and Harrisburg-based Hersha Hospitality Trust said they would return the money.

And on Thursday, Windtree disclosed to regulators that it, too, would repay its loan. The company — which reported a net loss of $27.5 million last year — had previously said it hopes to secure funding to conduct a clinical study on treating patients with a coronavirus-related lung injury.

A spokesperson for Windtree said the company had no further comment on the loan.

Some Philadelphia-area public companies said they were good candidates for the loans.

Malvern-based Neuronetics Inc., a commercial stage medical technology company that makes products intended to help psychiatric patients, received a $6.4 million loan on April 21.

The company said in an April 27 filing that it believed the loan request was necessary because of disruptions to business activity and “its inability to access other sources of liquidity.”

Neuronetics reported preliminary revenues of $12 million for the quarter ending March 31, and said it had $63 million in cash and cash equivalents. Last year, Neuronetics posted revenues of $62.7 million and a net loss of $29 million.

The company had 235 full-time employees to start the year. It said it was laying off some workers and furloughing others to reduce expenses amid the pandemic.

A spokesperson for Neuronetics said the company would provide additional details on the PPP loan during its first-quarter earnings call on Tuesday.

Horsham-based Strata Skin Sciences, a medical technology company that received a $2 million loan, said last week that it did not have a “substantial market value” or "substantial access to the capital markets.”

To conserve cash, management has deferred the payment of 2019 fiscal year bonuses, and its board has deferred second-quarter board fees, the company said.

Strata in March reported revenues of $31.6 million for 2019, up 5.8% over the previous year. It posted a net loss of $3.6 million, and said in its annual report that it had “incurred losses for a number of years and anticipate that we will incur continued losses for the foreseeable future.”

In January, Strata disclosed it had refinanced a $7.25 million bank loan. “This refinancing and new commercial bank loan facility is a testament to our financial strength and ability to generate cash flow,” CEO Dolev Rafaeli said at the time.

Other companies had also been losing money before the virus hit — not unusual for health-related businesses that have yet to win regulatory approval for their products.

Newtown-based Helius Medical Technologies Inc., a neurotech company with 19 full-time employees, warned investors in its annual report that it believed its existing capital resources would be insufficient to fund operations beyond May 2020. The company had just $5.5 million in cash as of Dec. 31.

“If we are unable to obtain additional financing as needed, we may be forced ... to cease or wind down operations, seek protection under the provisions of the U.S. Bankruptcy Code, or liquidate and dissolve our company,” the company told regulators on March 12.

Last year, Helius faced a setback when the Food and Drug Administration declined regulatory clearance for a device to treat traumatic brain injury.

In March, the company reported total 2019 revenue of $1.5 million and a net loss of $9.8 million.

On April 16, Helius disclosed it had received a $323,000 PPP loan.

The company is now considering returning the PPP loan, CEO Philippe Deschamps told Philadelphia Business Journal last week.

“We are resourceful people,” Deschamps said. “If you’d ask me was this our only option, I’d say of course not. We would have found another way to survive, but this was really, really welcome.”

He also said that the company had been running short on cash and that the loan would enable it to keep employees working on its FDA application. In addition, Helius couldn’t access public markets at the time because of federal securities regulations prohibiting stock sales ahead of earnings reports, he said.

Helius didn’t respond to a request for comment.

Some companies were boasting of strong balance sheets just weeks before applying for the government-backed loans.

In February, ADMA Biologics, a biopharmaceutical company based in Bergen County, N.J., received net proceeds of $88.5 million from a public stock offering. This “strengthened our balance sheet and enhanced our working capital position,” CEO Adam Grossman said in a March statement.

The company, which has 314 employees, received a $5.4 million PPP loan on April 16, records show.

It incurred net losses of $48.3 million last year and $65.7 million in 2018. The company said in its annual report that it expected “to incur substantial losses" into fiscal 2021, "and we may never achieve or maintain profitability.”

In Western Pennsylvania, the manufacturer Universal Stainless & Alloy Products Inc. received a $10 million loan April 17, the maximum allowed under the program.

“These funds have enhanced the company’s financial flexibility," chief financial officer Christopher T. Scanlon said during an earnings call a few days later.

He added that, as of March 31, the company had $41.7 million in available loans under an agreement with its bank.

Universal reported net sales of $58.5 million for the first quarter, down 2.9% from the year-earlier period. It had a net loss of $1.4 million.

“There is no doubt that our industry is highly stressed and uncertainty runs high,” CEO Dennis Oates said on the call, noting that the company serves struggling industries such as aerospace and oil and gas. “Customers tell us that they are still trying to make sense of conditions. Even so, they are taking a conservative approach to their ordering, buying when they have demand, but not much on speculation."