Station manager Brett Loft said 1,000 people had been evacuated from a club as well as Charing Cross hotel.
Fire brigades, using detection equipment, recorded a high level of gas in the atmosphere. It said 1,000 people from the nightclub and 350 residents and business personnel were evacuated.
A Network Rail spokesperson said: "Both Charing Cross and Waterloo East stations are now closed owing to a gas leak in a nearby road".
London Fire Brigade (LFB) said it was called to the scene at after high levels of natural gas were detected at the scene in Craven Street near Charing Cross station.
The Metropolitan Police said officers and the London Fire Brigade were working with the National Grid and other agencies at the scene.
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Cadent said the emergency services' cordon will remain in place until all safety checks have been completed.
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Revellers at Heaven nightclub were forced to leave and guests at the hotel moved to emergency accommodation as fire services responded.
There is severe disruption in London's West End due to a gas leak at the Strand.
A 150m cordon was quickly erected as engineers set to work.
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Rail services are expected to resume by noon, Southeastern railway said on its website.
"Gas engineers are working on isolating the leak and we'd asked people to avoid the area if possible".
"We will reopen the station as soon as we have clearance from emergency services that it is safe to do so". Literally chaos. Crush on the stairs.
An alarm sounded throughout King's Cross as commuters were evacuated when huge numbers attempted to travel through the station - one person tweeted it was a "nightmare" as pictures of people gathering outside the station emerged.
Services will be diverted into Victoria, Cannon Street and Blackfriars stations and some services may be delayed or cancelled as a result, Network Rail has warned.
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Strand, Northumberland Avenue and Trafalgar Square have been cordoned off by police.