In the second fault to hit the £7 million project since the gateway was re-opened last week, the upper bank of escalators has been switched off to prevent rainwater causing electrical problems.
Network Rail said the leaks were caused by a last-minute change of sealant between panels in the upper section of the glass roof, which had not dried before it started raining.
The firm said the original sealant was deemed to have been “unaesthetic”, which led to work starting on replacing it.
The setback follows one of the upper escalators being taken out service hours after the steps were re-opened because of a fault with its emergency brake. The project was completed five years late.