Nauru's president Baron Waqa fired chief magistrate and supreme court registrar Peter Law yesterday and ordered him to leave the country.
When Justice Eames issued injunctions to try to stop Mr Law's deportation, his own visa to return to the country this morning was cancelled.
Justice Eames says the Nauruan government did not agree with rulings made by Mr Law, which stopped the government from deporting three resident foreign nationals - two of them Australian.
The cases involve two Australian businessmen who had been declared "prohibited immigrants" by the country's justice minister and given a week to leave Nauru.
One of the men is Rod Henshaw, a former ABC broadcaster who also worked as a media adviser to the Nauru government.
It is believed he had been running a bar at a government-owned hotel in Nauru.
To not to follow the chief judge's orders and then to cancel his visa really throws any concept of justice out the window. It's really outrageous.
The residents appealed to the courts and Mr Law granted an injunction against their deportation.
Justice Eames says the decision was "politically motivated, designed to have the decisions overturned by a new magistrate and amounted to an abuse of the rule of law".
He says he has had no contact with the Nauruan government, but he believes the timing and comments from the government about the cases are revealing.
"I can only draw one conclusion," Justice Eames said.
"The decision was taken to simply remove [Mr Law] from his position and replace him with someone else."
Justice Eames says it is an "extremely busy week" for the Nauru court, with about 60 cases involving asylum seekers accused of rioting due to be heard.
"I imagine [the Nauruan government] will seek to have someone take Mr Law's place - they may well have difficulty in doing that," he said.
"I can't imagine that any lawyer knowing these circumstances would be prepared to accept the posting."
The country's solicitor-general, Steven Bliim, has now tended his resignation, and a new resident magistrate from Australia has been appointed.
Melbourne-based solicitor Andrew Jacobson arrived in Nauru today.
In court this afternoon, Mr Jacobson adjourned a decision on whether the deportation injunctions issued by Mr Law last week will be upheld or dismissed.
Former chief magistrate decries 'contempt of court'
Mr Law is now back in Brisbane and says Mr Waqa's actions are clearly in contempt of court.
"To not follow the chief judge's orders and then to cancel his visa really throws any concept of justice out the window. It's really outrageous," Mr Law said.
"It was a very comprehensive injunction and it specified the various authorities, including the airlines and the police and there were copies issued to the minister of justice and I believe the president, so it's hard to imagine why it was ignored."
Mr Law says he has been given no reason for his deportation, but the president has said it is related to allegations of misbehaviour against Mr Law by a former member of staff.
He says he had a disgruntled staff member who he suspended because he became abusive, but he denies that is the reason for his expulsion from Nauru.
"The timing of this makes it very obvious in my mind what this is all about," he said.
"My own assumption is this: I've issued orders against the minister for justice - decisions that he has made concerning two foreigners who've been declared prohibited immigrants.
"They've got a right to judicial review, which they sought - that is to review the minister's decision. And they had a right to apply for an interim injunction. Those were the orders that I gave and [that] I had stood over until today.
"That's not going to take place, of course, because I am not there."
Opposition says government has 'lost the plot'
Nauruan opposition MP Mathew Batsiua says the move is a great interference in the independence of the country's judiciary.
"It's another example of the lengths this government will go to to get its way," he said.
"The letters that they issued to the resident magistrate didn't spell out any reason, they just basically terminated his contract because they can."
He says there is no plan as yet for a new magistrate or chief justice.
"That's a question for government. How are they going to fill the void?
"They've lost the plot. They've interfered in the media, now they've interfered in the judiciary.
"By disregarding the independence of the judiciary they are disregarding the constitution."
Justice Eames says the actions have implications for the Australian Government.
"A government which has got such close ties with Nauru and has had for many decade - I would have thought they'd have more than a passing interest in such instability in the judicial system in the Pacific region," he said.
However, Justice Eames says he cannot see how there would be any benefit to the Australia Government in Mr Law's removal.
He says he cannot be replaced as the country's chief justice.
"I have an appointment which under the [Nauruan] constitution runs until the age of 75. I'm currently 68," he said.
"I can't be removed except by a vote of two-thirds of parliament on the proven grounds of misbehaviour, and there has been no suggestion of that."
Government's actions not consistent with law: lawyers
South Pacific Lawyers Association president Ross Ray QC says his organisation was "extremely surprised and very disappointed" with the government's actions.
"The conduct of the Nauruan government seems to be absolutely inconsistent with a commitment to the rule of law."
He says the range of cases before Mr Law that have not been fully heard - including those involving asylum seekers accused of rioting - need to be completed.
"I think Minister Morrison has suggested that...the Australian Government was seeking advice from the Nauruan authorities on how the cases would proceed," he said.
"That, of course, is a matter of significance. It's important that those people have access to a justice system.
"But what's concerning is the fact that this appears not, as Minister Morrison has said, to be something much about internal Nauruan politics and issues, but broader than that.
"Not related to the asylum seekers but more broadly related to ensuring there is an independent judiciary to enforce the rights of all parties."
The Law Council and Bar Association has raised concerns about the deportation of the men.
The council says Australia has a responsibility to ensure the rule of law operates in Nauru, particularly given the arrangements it has made regarding the processing of asylum seekers.