Services from Moorgate to Finsbury Park where suspended all day after augers from piling work near Old Street station fell into the tunnel.
Transport bosses at First Capital Connect praised quick-thinking staff who averted a major incident .
The driver of a train reported muddy water pouring onto the roof of his train north of Old Street station on Friday.
All rail services were immediately stopped and augers were later found on the floor of the tunnel.
The company said: “Thanks to the quick actions of railway staff, this was prevented from becoming a more serious incident.
“However extensive repairs will now have to be made to the tunnel before the line can reopen.”
The Rail Accident Investigation Branch and British Transport Police are investigating the incident while Network Rail is working with specialist tunnelling contractors to assess the damage.
The piling contractor involved in the incident was working on the foundations for a residential development.