The flagship of Russia's northern fleet has been ordered back to port, prompting a scare over the safety of the ship's nuclear reactor.
The nuclear cruiser is normally based in Murmansk
The commander-in-chief of the navy was initially quoted as saying that the nuclear cruiser Peter the Great "could go sky high at any minute".
But Vladimir Kuroyedov later denied any threat to the reactor.
He said the ship's living quarters were unsatisfactory and gave the captain two weeks to fix the problem.
The BBC's Sarah Rainsford in Moscow says Admiral Kuroyedov's own job is thought to be on the line - and military analysts suggest the decision to take this flagship out of service may have more to do with infighting among Russia's naval elite than with any genuine danger on board.
It could also be part of a campaign for greater funding from government.
Admiral Kuroyedov's remarks are thought to be aimed at the ship's captain, Rear-Admiral Vladimir Kasatonov.
The captain's uncle, himself a retired admiral, was recently highly critical of Admiral Kuroyedov in a court hearing on the sinking of a nuclear submarine last year in which nine sailors died.
The 40-year-old K-159 submarine sank in the Barents Sea in bad weather on 30 August as it was being towed to a scrapyard.
But Stephen Saunders, author of Jane's Fighting Ships, told BBC News Online that Admiral Kuroyedov's decision was probably based on a number of factors, including a desire to shore up discipline in the navy by giving a public reprimand to one of its premier ships.
There was quite likely also something genuinely wrong with the ship, but the fact that the captain had been given two weeks to bring it up to scratch suggested this was not serious or nuclear-related, he added.
"He's clearly found a number of things wrong," Mr Saunders said.
"Whether what he's found relates to safety issues is difficult to say."
The Northern Fleet has been plagued by a series of such incidents beginning with the Kursk submarine disaster in the same sea in August 2000.
Admiral Kuroyedov said he had ordered the ship back to port after an inspection during naval exercises in the Barents Sea last Wednesday.
RUSSIA'S NAVAL DISASTERS
August 2000: Kursk nuclear submarine sinks in Barents Sea, killing all 118 crew. After a two-year investigation, a faulty torpedo is blamed
August 2003: Decommissioned K-159 nuclear submarine sinks, also in Barents Sea. Nine of its 10 crew are killed
February 2004: Ballistic missiles fail to launch from a submarine during military exercises in Barents Sea
"In those places on board where the admirals actually go, everything's fine, but where they don't go, everything's in such a state it could go sky high at any minute... And by that I also mean the state of the nuclear reactor," he was quoted as saying.
"It is this attitude to the upkeep of their ships on the part of commanders that is leading to the collapse of the fleet."
But several hours later he said media reports on the threat to nuclear safety were untrue.
"Reports from certain media sources that the Peter the Great is in a dangerous state which could present a nuclear threat have no truth in them whatsoever," he told Russian media.
The Peter the Great is normally based near the northern port of Murmansk, but the ship's current location has not been specified.