The Nuevos Ministerios station, which serves three lines of Madrid's metro system as well as six regional commuter railway lines, was closed just before 6.00 pm (1700 GMT) after the package was located at one of its entrances, the spokeswoman said.
The station reopened about an hour later after a police bomb squad concluded that the package was not dangerous.
"It was a false alarm. There was nothing inside the box which could explode," the spokeswoman said.
Yesterday, police ordered the evacuation of 300 staff at the offices of the El Pais daily after a man delivered a suspect package around two hours after the Paris attack.
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Security guards became suspicious because the man refused to take the package to a rear entrance and insisted on leaving it at the main entrance.
But staff were allowed back into the building about two hours later after police determined the package was not dangerous.
Police said a man claiming to be carrying a bomb in his backpack was arrested, but nothing was found.