The difficulties facing online lenders are another example of the dysfunction and disorganization that have slowed down the flow of loans to small businesses, even as President Trump has insisted that the program is going well, with only a few small glitches.

Financial technology companies like PayPal and Square, and smaller companies that focus on small-business lending, like Kabbage and OnDeck, have specialized in giving loans to the businesses that are the focus of the government program — those with fewer than 500 employees — and doing it more quickly than banks. Many of the lenders have expressed frustration that they have been shut out when they feel they could be the most useful.

“Every five minutes I’ve been refreshing the Treasury page like a maniac,” said Sam Taussig, the head of global policy at Kabbage, one of the largest online lenders for small businesses. “The businesses that we serve on Main Street, they only have about 10 to 12 days of cash on hand, and we are well past that in many places.”

The Small Business Administration and the Treasury Department, which are overseeing the loans program, didn’t respond to requests for comment about the online lenders. S.B.A. officials have said they are working to iron out any issues slowing the flow of money to business owners.

The lenders want to help distribute the $349 billion in loans the government is giving to small businesses to help them make payroll and cover other costs during the pandemic. The loans have generous terms, including a low interest rate and forgiveness for portions spent on fixed costs like rent and paychecks for employees who aren’t working.