Team Tonga Chef de Mission 'Amanaki Fakakovikaetau, who is also a member of TASANOC's Executive Committee, said the government only told them last Wednesday it would pay for the flight, which is scheduled to leave on Thursday.
He said the original payment deadline from Air Vanuatu has since passed but the airline have kept the door open while they wait to hear from the government.
"But they've also been negotiating how we're going to do this payment and we're still waiting for the confirmation and the letter from government that they are going to do that," he said.
"There are some other things that the government needs from us, from TASA, in order for them to sign or send the money and I think we should be ready but all the government needs from us up until now (is) to be submitted to them this afternoon (Thursday) and hopefully they will discuss it in the cabinet (on Friday)."
Dr Fakakovikaetau admitted the recent election has delayed the process, with a permanent government still yet to be formed, and said the administration wanted assurances the athletes travelling to Vanuatu would not just be making up the numbers.
"We have sat down with the sports minister and the minister of internal affairs, in which the sports ministry is under that, which they do need some sort of athletes or team profiles and see their preparedness and are they ready to get a medal for Team Tonga," he said.
"The request was made months ago and then finally the government did tell us what they want, what they need so we worked with them again in order to comply with their requirements...to satisfy the government that they're going to use the taxpayers' money to send a team to compete and win a medal."
Dr Fakakovikaetau said if the charter flight falls through it could put Tonga's attendance at the Mini Games in jeopardy.
"That will be a big step for us to climb and the airfare now is maybe two times or three times the original cost...because there are two ways: either Air New Zealand or Fiji Airways but hopefully we will pull through this and Air Vanuatu are still happy to come and pick us up."
Tonga is intending to send athletes to compete in 12 of the 14 sports on offer at the Mini Games.