This was despite a court order that he attend an appeal hearing against the deportation order issued on Thursday, the newspaper said.
The deportation is the latest move in a crackdown on the media in Fiji since military commander Frank Bainimarama seized power in a coup in late 2006.
Fiji's rulers have faced growing international criticism over the slow progress in returning the South Pacific island nation to democracy.
"Our people have been under constant threat and intimidation for the last 18 months."
editor of Fiji Times
Murdoch's Australian publishing arm, News Ltd, also condemned Hannah's deportation as the latest threat to press freedom in Fiji.
Netani Rika, editor of the Fiji Times, said his newspaper had always been a watchdog on government policies regardless of who was in power and would not soften its stance despite the latest deportation.
"We've been a strong critic of, I wouldn't say government, but of government policies dating back more than 20 years," he said.
"I think, yes we are recognised ... as the unofficial opposition in the country."
Rika said Fijian journalists have been harassed by the government for 18 months adding that the latest deportation was part of a campaign to silence media criticism.
Helen Clark says the expulsion will spark
'regional and international concern' [AFP]
"Our people have been under constant threat and intimidation for the last 18 months. Mr Hannah is not the first journalist to be removed from his home," Rika told Australian radio.
"All I can think of right now, that it is an attempt to intimidate the media, yes," he said.
"For us at the Fiji Times, it just means that we now know that the government will not take dissenting views lightly, but it also means that we have an even more important role to play to ensure that the views of all people in this country are made known, including the views of the government."
The deportation comes after another Australian, Russell Hunter, publisher of the rival Fiji Sun newspaper, was deported in February for criticising Bainimarama's government.
The Fiji Sun said in an editorial on Friday that "the night-time abduction of Fiji Times publisher Evan Hannah marks yet another sorry milestone on the interim government's road to disgrace".
"Make no mistake, these deportations are the precursors to stringent and punitive media controls ...," it said.
"This will give the interim government what it has long craved: total control over what the people of Fiji are permitted to know and even discuss publicly. It will give the regime the power to act in secret."
Bainimarama has promised to hold free and fair elections by early 2009, but Clark said the deportation was not conducive to creating the kind of environment needed for such polls.
New Zealand's acting high commissioner in Suva, Caroline McDonald, was seeking an explanation from the Fiji government
But Clark said "no reasonable explanation was given for Mr Hunter's expulsion earlier in the year, and we cannot see any basis for any reasonable explanation in the current case".