The Daily Mirror reporters were arrested at the Stonebridge Park depot, in north-west London, after they were seen acting suspiciously by staff.
A Mirror spokesman said the stunt was a justified follow-up after its journalists managed to place a fake device on a nuclear train in 2006.
Police confirmed two men had been arrested on suspicion of trespass.
Security lapses
Officers were still searching the depot, said a British Transport Police spokesman.
A Mirror spokesman said: "Last year Mirror journalists attempted and succeeded in planting a fake bomb on a nuclear train, which highlighted serious security lapses.
"We therefore felt that it was a legitimate and justified journalistic exercise to repeat the action in the interests of public safety.
"We are happy to see that the security procedures have now improved."
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