Last week, the governing council held an emergency meeting to look into the suspension of the Vice Chancellor by the executive committee.
The council found due process had not been followed and reinstated Pal Ahluwalia.
Incoming Chancellor and Nauru President Lionel Aingimea was instrumental in Professor Ahluwalia's reinstatement.
Mr Aingimea said the council would reconvene with last Friday's not closed.
He said the meeting had simply been recessed until the next one which was yet to be scheduled.
Meanwhile Pro Chancellor Winston Thompson, who headed the Executive Committee to suspend Professor Ahluwalia, claimed there were now moves by the council to remove him.
But Mr Thompson said he would challenge any motion for him to vacate his council seat as chair.
During last week's meeting, the council voted for Mr Thompson to recuse himself from discussions and Mr Aingimea chaired the meeting.
Mr Thompson was also asked to step aside as council chair while investigations against Professor Ahluwalia were carried out.
Mr Thompson said he was also not allowed to present a paper he had prepared for the meeting.
Earlier, Samoa had signaled it would seek the removal of Mr Thompson, with their preferred replacement being Lionel Aingimea.
In a letter addressed to all council members, Education Minister Loau Keneti Sio said his government's position "is that council instruct the Pro Chancellor to cease and desist from carrying out this investigation into the charges of material misconduct against the Vice Chancellor as these are substantially to do with issues referred to the commission"
Loau said Mr Thompson's actions countered the "council's intent and resolutions to address the issues investigated and reported on by the BDO (accountancy firm) through a process of institutional reform under the auspices of the commission".
"In the event that the PC does not comply, that council will begin proceedings to remove him from office."
Tonga's Education Minister Siaosi Sovaleni said he was disappointed at Mr Thompson's treatment of Professor Ahluwalia.
In a letter to Mr Thompson obtained by RNZ Pacific, Mr Sovaleni said the pro-chancellor's behaviour had "reciprocated" the council's efforts to settle the issues at the university.
"You continue to demonstrate an antagonising attitude towards the VCP," he said. "It is disappointing and disheartening to witness these matters surfacing at a time when countries are in crisis and our region are focusing on measures to address the Covid-19 pandemic.
"Not only are we severely hindered by our inability to convene a council meeting to discuss these issues personally, under such circumstances, but it is an untimely and ill-conceived attempt to force us to make impulsive responses and decisions."
The minister said the Tongan government wanted the council and Professor Ahluwalia to focus on the safety and welfare of students and staff as well as the future of the university.
Mr Sovaleni said the "quarrelling between the pro-chancellor and VCP must end as the council demands professional behaviour and responsible leadership and management at all times".
At last week's meeting, 22 council members also voted for the recusal of two other members of the Executive Committee: Deputy council chair Aloma Johansson and chairman of the Audit and Risk Committee, Mahmood Khan.
The Fiji Sun newspaper reported only seven council members voted against the recusal while two abstained.
"It is understood it took three hours to convince the trio to recuse themselves from the meeting," the report stated.
"A vote was taken to prove that the majority wanted them to vacate the meeting."