British Transport Police said specialist teams were dispatched to the station and a small cordon was put in place.
The station remained open and train services continued to run, though the taxi rank on Station Approach and the bike storage area was closed.
A spokesperson for the British Transport Police said it was “too early” to say whether the suspect packages were linked.
“British Transport Police were called to Waterloo station at 11.40am today following reports of a suspicious package,” the spokesperson said.
“The item is currently being assessed by specialist teams.
“Cordons are in place however train services continue to operate as normal at this time.”
Meanwhile, the Metropolitan Police said they were called to a report of a suspicious package at London City Airport’s headquarters in Aviation House at 12.10pm.
The building was evacuated and specialist officers were at the scene.
London City Airport said flights were not disrupted and it was operating as normal. The DLR, which has a station at the airport, was temporarily suspended but later resumed normal service and roads around Aviation House were cordoned off.
Scotland Yard later said they were called to reports of a suspicious package at Compass Centre, which houses Heathrow Airport’s administrative centre, around 10am.
A spokesperson for Scotland Yard said the building was evacuated and the package “made safe”.
Heathrow Airport continued to operate as normal during the incident, which police are treating as a “criminal act”, a spokesperson for the airport said.
“Earlier today, police responded to reports of an incident in the Compass Centre. Police response teams and the emergency services attended quickly, enabling colleagues to evacuate safely without injury.
“Heathrow Airport remains operational, flights are not impacted and passengers are able to travel as normal. The police are treating this as a criminal act and we will be assisting with this investigation.”
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