BBC Sport has learned $3.7m (£2.9m) of travel grants owed by the Rio 2016 organising committee to national Paralympic bodies are two weeks late.
Several smaller countries took out loans to send teams to Brazil - which the IPC covered with emergency funds.
The IPC is now thought to be considering legal action against the Rio 2016 organising committee.
The Rio Paralympics went ahead in September, but only after budget cuts to venues, the workforce and transport caused by recession and extra spending on the Olympics.
An initial instalment of delayed grants covering the costs for athletes and officials was paid.
But the second payment is now overdue, risking another blow to the legacy of South America's first Games.
"We're hugely disappointed that the second instalment of the travel grants, just like the first set, have not been paid on time by Rio 2016 and are urgently seeking a resolution to this issue from all parties concerned," IPC spokesman Craig Spence said.
"The IPC has stepped in to keep these smaller NPCs [national Paralympic committees] afloat.
"The longer this situation goes on, the more likely it is that other NPCs come forward asking for financial support from the IPC."
Rio 2016 officials are understood to have told the IPC that they cannot pay because they themselves are owed money from the city authorities.
Furthermore, their accounts have been frozen by a court following a lawsuit filed by two suppliers who say they have not been paid.
The IPC has now sent a letter to Rio mayor Eduardo Paes asking for his help.
In August Paes secured an additional £36m of funding and £24m in sponsorship from state-run companies after an injunction was lifted that had blocked further state aid for the Paralympics
"Overnight we have sent a letter to Rio mayor Paes, who was hugely supportive of the Paralympic Games, asking him to step in and intervene" Spence said.
The International Paralympic Committee (IPC) is facing a major new financial crisis linked to Rio 2016.