The IRL confirmed the TNRL had been kicked out of the world body after a special general meeting last week backed an earlier board decision by nine votes to five.
Only full members of the world governing body could vote.
RNZ Pacific understands Fiji, Samoa and the Cook Islands voted against the move to expel the TNRL.
The IRL only needed 25 percent of the vote to support the board's resolution.
IRL global operations manager Danny Kazandjian said although they were pleased the majority of members supported the move there was still a wish that it never got this far.
"It's taken hundreds of man hours, quite a lot of resources, and we're now looking along with the members to move forward with a new Tonga governing body so Tonga Rugby League can continue to contribute in the magnificent way that it has over the last few years," he said.
"I think it's important to point out that Tonga Rugby League are not excommunicated from the game, it's just the narrow question of the governing body Tonga National Rugby League," Kazandjian said.
He said Tonga should see the situation as as an opportunity for growth.
"We expect to get another application from another governing body in the not too distant future and then work with the Tongan rugby league community to rebuild locally, rebuild the relations internationally, and to continue contributing to the international game to the extent they have over the last couple of years."
The TNRL had been suspended since October 2019, after it sacked national coach Kristian Woolf over disagreements around control and finances, which led players to threaten a boycott of the World Cup 9s and end of season tests.
In February, the IRL board made the decision to expel the TNRL after the long-running governance battle.
Kazandjian believed the IRL did everything possible to ensure a thorough investigation and found the TNRL represented a threat to the objectives of the international body.
Their hand was forced further when the UK's RFL became concerned about the situation ahead of their scheduled tests with Tonga.
"The International Rugby League is here to support national federations but when one of our member federations lodges a formal complaint against one of it's colleagues, we are constitutionally obliged to react."
"I think the initial reason for the suspension was that TNRL represented through it's own actions a material threat to the IRL being able to fulfil its objectives, to develop and disseminate and support the sport of rugby league internationally."
"Once they were suspended in September, we launched an investigation into Tonga rugby league, not just TNRL, but Tonga rugby league because we wanted to understand the complexity of the relationships and how they manifested themselves in the issues that evolved over the last few months."
Kazandjian claimed the TNRL were co-operative at the outset of their investigation, but from mid-December "they ceased co-operating which proved problematic".
Following the initial investigation, Kazandjian said the decision was made not to expel the TNRL but to work with them to help introduce reforms.
The IRL did not investigate any financial audits of the TNRL accounts and the decision was based on governance and a lack of confidence in the administration, he added.
"Our investigation included interviews, surveys over many months, questionnaires, consultations with all of the rugby league clubs that participate, with TNRL itself, with the diaspora of organisations, with the national team players, with national team staff, with government and with the Tonga Sports Council.
"Our recommendations in a nutshell were to more accurately reflect the state of Tonga rugby league or the balance of constituents in Tonga rugby league that exist today."
Recommendations made by the IRL included involvement from the diaspora organisations, player representation and rugby league clubs in Tonga.
Kazandjian added that having a player-led governance would also be encouraged.
"The elite national team players are responsible for the lions share of the revenue."
"Player led governance is quite normal and is a popular theme in international sport governance, so rather than them taking drastic measures into how the sport is run, we try to encourage them to contribute in a systematic structured way as part of that governance framework rather than just being national players," he said.
Members of the TNRL argued there were already representatives of the sport including past players on the board, but Kazandjian said they weren't representative of the current national team.
The TNRL had stated they were willing to take the case to the Court of Arbitration for Sport.
Kazandjian said that was a decision left to the TNRL.
"It's up to them to decide what they want to do. TNRL is an organisation that exists, it's just no longer our member," he said.
Tonga's next match was scheduled in June against New Zealand but has since been postponed due to the Covid-19 coronavirus pandemic.