Fiji's military strongman Voreqe Bainimarama said the "illegal extraction" took place last week, when the patrol boat plucked senior army officer Lieutenant-Colonel Tevita Mara from waters off Fiji's Kedavu island.
Bainimarama described Mara, who Tongan officials said was now staying at the royal palace in Nuku'alofa, as a fugitive whose getaway was an act of a "despicable nature".
"The Fijian government takes strong exception to such breaches of Fiji's sovereignty," Bainimarama said in a statement published on the official government website on Monday.
Former senior army commander
Mara, a relative of Tonga's King George Topou V and son of the late former Fiji prime minister Kamisese Mara, was a senior army commander in Fiji who helped Bainimarama seize power in a 2006 coup.
He was charged with plotting to overthrow the government earlier this month and was on bail when he fled to Tonga.
Bainimarama, who seized power in a 2006 coup, said Suva would seek Mara's extradition and Fiji police were investigating who helped him escape.
He said the close relationship between Fiji and Tonga should not be compromised through a "conspiracy by a handful of self-interested individuals".
The Tongan government said on Friday that its patrol boat responded to a distress signal off the Fijian island of Ono-i-lau and rescued one person.
"The rescued passenger has been brought to Nuku'alofa, where arrangements have been made for his accommodation by the royal household office in deference to his rank," the statement said.
It added that Tonga's King George Topou V was travelling in Europe, but had been kept fully informed of events.
We won't interfere
Tonga's Prime Minister Lord Tu'ivakano said Monday that the Tongan courts would determine any application for Mara's extradition without political interference.
"Fiji's domestic affairs are her own and His Majesty's government has no interest in bringing undue influence," he said in a statement.
While Fiji and Tonga are separate nations, there are close ties between their ruling elites.
Tu'ivakano said any suggestion that the monarch's offer of hospitality to his kinsman Mara amounted to an offer of immunity from the law was "an offensive breach of protocol".
Footage purporting to show Mara was posted on YouTube over the weekend, in which a man who appears to be the fugitive officer said he fled Fiji after learning of a plan to imprison him without trial on "trumped up" charges.
"When I was rescued by the Tongan navy, I asked to be brought to Nuku'alofa where, under the sure protection of King George's government, I shall be able to tell the truth, without fear of retribution, about the tragic oppression which stifles my beloved land," he said.
"When this hateful dictatorship has been eradicated, all of us who once served it shall answer to the Fijian people for the part we played and I will gladly submit to their verdict."
New Zealand Prime Minister John Key said Wellington was closely monitoring the situation, describing Mara's rift with Bainimarama as a symptom of the Fiji regime's fragile nature.
"Tevita Mara is the guy that was Bainimarama's right-hand man when he undertook the coup back in 2006, so the fact that he's jumped ship is a very interesting development there," he told TVNZ.
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