The TRU signed a tripartite agreement with World Rugby and the Tonga Government on Friday , after the global governing body had threatened to pull all financial support.
The new partnership will see a Joint Management Committee take charge of the Union until long-standing governance issues are resolved.
Inoke Afeaki said the TRU had been in a "real mess" for a long time and World Rugby should have intervened earlier.
"I think they're whipping a dead horse," he claimed.
"I really think they'll end up in the same space in 15 years time having done another complete cycle of trying to give Tonga some space to follow its constitution."
The governing body suspended funding to the TRU earlier this year before issuing a final ultimatum but Afeaki said it was too little too late.
"They've allowed it to continue for way to long. They stopped the funding, which in my view they could have done that two or three years ago," he said of the original suspension.
"But they finally stopped it. Does that solve the issue? Not really - it just puts a halt and puts those who have been voted into positions into hibernation and they will stay there."
Among the conditions for signing the tripartite agreement, Fe'ao Vunipola has agreed to step down as Interim CEO of the Tonga Rugby Union after five years at the helm.
However the former test hooker remains influential as Vice President of the TRU, with MP Siaosi Pohiva having succeeded his late father and former Prime Minister 'Akilisi Pohiva as President.
"The dynamics that I see is awkward," suggests Afeaki, who played 24 tests for Tonga between 1995 and 2007.
"When I was in Tonga the government at the time and Fe'ao [Vunipola] were from the same political party, so the alignment there was the government is very supportive of rugby and pretty much had an empty cheque-book to get help from the government. Now that has changed so the government is not going to help Tonga Rugby."
Afeaki returned to New Zealand in January after a three-year stint working for the Tonga Olympic Committee and Tonga Sports Council.
He also had a brief stint as manager of the 'Ikale Tahi and is scathing of his former international team-mate Vunipola and his supporters, who have been in charge of rugby in Tonga for the past five years.
"They've had the full reigns of the rugby union for a long time and they chose to do very little, not even the bare minimum," he claimed.
"They're lucky they had a bunch of staff with the Tongan 'Ikale Tahi team that Toutai Kefu managed to gather and they were basically doing everything they needed to get done with regards to getting the team to a country and playing, and that was co-ordinated with World Rugby direct with the 'Ikale Tahi management."
This is not the first time the governance of Tongan rugby has faced scrutiny.
The Tonga Rugby Union was established in 2012, in response to concerns over the application of the former Tonga Rugby Football Union's constitution.
Inoke Afeaki believes the current constitution is sound but argued that the democratic process tended to favour popularity over competence when it comes to key leadership positions.
"The one thing that's flawed in the voting process is that you can vote for anyone at the end of the day and if you put your faith in someone that can't do the work then that's the bed you make, everything can all fall apart," he said.
"And if they're ok and staying in that position it hits the critical mass where the players become disillusioned and we're left in a position that we're in now."
The problem is not unique to the fifteen-a-side game.
"Having spent three years in Tonga and spending not only time with rugby union but all of the other sports they all have similar issues and it's to do with their governance."
Afeaki represented the 'Ikale Tahi at three Rugby World Cups but fears Tonga could struggle to make it to France in 2023.
"I really don't think World Rugby care," he claimed.
"They do have other countries on their sights that can replace Tonga in competitions so it's just a matter of time if Tonga fails to prove that it can do the job properly.
"World Rugby can't be baby-sitting Tonga all the time...then it will be Romania or another South American country. Tonga's just throwing the opportunity away and more kids are going to play rugby league."