The package was located at one of the entrances to the Nuevos Ministerios station, which serves three lines of Madrid's metro system as well as six regional commuter railway lines, just before 6.00 pm (1700 GMT), the spokeswoman said.
"The station was evacuated and police are investigating," she said without giving more details.
Services on some stations of the three lines which pass through Nuevos Ministerios station, one of Madrid's busiest, were partially disrupted, a Madrid metro system spokesman said.
Earlier 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.
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 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.
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