Westminster underground station was also closed off at Whitehall by cops shortly after the alert on King Charles Street at rush hour.
Pictures posted on social media show the busy district in Central London closed off, with buildings being emptied.
TfL wrote on Twitter: "A3212 Whitehall is CLOSED in both directions between Parliament Square and Horse Guards Avenue while police investigate an incident. Use other routes and expect delays."
The security alert came before protesters prepared to march through Westminster as part of the Million Mask March.
Thousands are descending on the streets of major cities around the world for Bonfire Night, led by "hacktivist" group Anonymous.
However, police have said the closures are not related to the march.
Eyewitness Thomas Danielian said: "Im at Parliament Square. Suspicious package. Whitehall closed. All buildings empty. Westminster station closed too."
ITV political correspondent Carl Dinnen added: "Whitehall closed from Parliament Square to Horseguards as police examine a suspicious package."
More to follow…
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