Barbican Station was closed and the area around it was placed on lockdown as police dealt with a suspect package.
Armed police were reportedly seen sealing streets off during the incident on Sunday morning.
The British Transport Police tweeted to say that an unattended bag on a train had been deemed safe.
The force added that an unattended item on a bridge was also being investigated.
Barbican Station has since reopened, Transport for London said, and the cordons ae understood to have been lifted.
A witness tweeted: "Barbican closed off from a suspect package, all clear now. @cityoflondon police doing a good job with the situation. #wearenotafraid #london".
Another added: "Armed Police sealed off #Goswellroad #barbican looks serious".
The City of London Police could not be reached for comment but were understood to be attending.