A program intended to wipe away the student loans of qualifying public servants has rejected more than 99 percent of those who applied, according to a government audit that found that “fragmented” management and “piecemeal” operating instructions had contributed to the failure to forgive more debt.

The Education Department said last week that 28,000 borrowers had submitted applications to have their debts canceled since the public service loan forgiveness program began accepting them a year ago. Only 96 were approved, the agency said. More than 70 percent were rejected for not meeting the eligibility requirements. Most of the rest had left necessary information out of their applications.

In its report on Thursday, the Government Accountability Office said major administrative failings had left both the program’s administrator and borrowers in a state of confusion about the program’s rules.

To get their remaining balances forgiven, applicants must spend at least a decade working for government agencies or certain types of nonprofit organizations; they also must make 120 qualifying monthly payments on their federal student loans. More than 1.2 million borrowers have sought to have their employment certified for eligibility in the program, the accountability office said.