The ruling, issued on Friday, clashes with a recent suspension of the TNRL by the world governing body - Rugby League International Federation, (RLIF) - which came after Tonga's then-acting Prime Minister Semisi Sika declared the local body had lost the trust and support of the government, clubs and players.
Mr Sika has since lost a prime ministerial vote and finds himself on the outside of government, yet the RLIF still backed his call to place an interim administration in charge of the sport ahead of upcoming internationals against Great Britain and Australia.
Mr Sika was also the President of the previous TNRL that was dissolved by court order because of concerns over financial mismanagement and unaudited accounts.
The suspension led to the TNRL, whose board was elected afresh this year, launching legal action against the Tongan government and the RLIF-endorsed interim body Tonga Ma'a Tonga Rugby League or TMTRL.
On Friday Justice Laki Niu declared the government and the TMTRL were "restrained and prohibited" from making decisions involving Tonga's popular national team, including around coaching, staff, management and apparel.
Last month the TNRL sacked national coach Kristian Woolf over disagreements around control and finances which led to a group of players, including Jason Taumalolo and Andrew Fifita to threaten a boycott of the country's upcoming games.
It has since emerged that Woolf asked his players to sign statements regarding a boycott and he was in communication with Semisi Sika over the creation of the new TMTRL.
Woolf has denied any wrongdoing and said the players were "strong and intelligent young men" who did not need his help to make decisions.
The status of upcoming rugby league internationals continues to be uncertain with the local courts and RLIF seemingly at odds with who is in control of the team, which has had unprecedented success and exposure in recent years.
Tonga is scheduled to meet Great Britain in Hamilton on 26 October and Australia on 2 November in Auckland.