Earlier this afternoon, the London Fire Brigade said it was investigating reports of smoke coming from the building, but crews left shortly after their arrival.
However, National Rail said disruption to First Hull, Grand Central, Great Northern and Virgin East Coast trains were likely to continue until "at least" 5pm - just as the great Bank Holiday getaway began.
"There is no firm estimate of how long disruption will last," it added.
Twitter users posted pictures of hundreds of passengers lingering outside the station.
The news came hours after hundreds of passengers were evacuated from Victoria Station this morning, thanks to another fire alert.