Trains, trams and buses were halted or rerouted as the operation to dispose of the British 500-kilogramme (1,100-pound) bomb found more than 70 years after the war got underway.
Authorities have declared an exclusion zone with an 800-metre (yard) radius around the site located just north of the central railway station, a transport hub that on a normal day is used by 300,000 passengers.
Arriving from Leipzig on a day trip to Berlin, Japanese tourist Yamamoto looked bewildered as he was told of the operation at the railway station.
"We didn't know anything about the bomb," he told AFP.
The exclusion zone covers the train station, an army hospital, the economy ministry, an art gallery and a museum as well as part of the BND intelligence service's new headquarters.
Many thousands of residents and employees have been ordered to stay clear of the area and not return until police give the all-clear.
Among them were workers at the economy ministry who were told to work from other offices or from home, or were simply given the day off, a spokeswoman said.
Police also went house to house to check the zone has been completely cleared before the bomb disposal experts began their work.
Temporary shelters have also been set up for those affected by the evacuation.
Esen Coskon, 50, who was at one of the shelters with his 22-year-old son, Furkan, said he learnt of the evacuation from the media and police, who had sent leaflets to every home.
Coskon said the operation was deja-vu, with a similar one in 2013 also affecting the area around the main railway station.
Angela Merkel's chancellery building and the Reichstag (parliament) lie just a few hundred metres to the south of the no-go zone and can keep operating as usual.
3,000 bombs in Berlin
More than 70 years after the end of the war, unexploded bombs are regularly found, a potentially deadly legacy of the intense Allied bombing campaign against Nazi Germany.
In the biggest post-war evacuation, at least 60,000 Frankfurt residents were forced to leave their homes last September so that an unexploded 1.8-tonne British bomb dubbed the "blockbuster" could be defused.
Some 3,000 such unexploded bombs are believed to still lie buried in Berlin, a city of three million people, where disposal squads are well-practised in defusing them and other ordnance.
It was unclear how long the bomb disposal squad would take to disable the bomb found during construction work on Heidestrasse in the district of Mitte.
"We're talking here about a bomb that measures about 110 by 45 centimetres, so it's a hefty heavyweight blaster with the potential to cause severe damage in the centre of town; that's why we are going about it very very carefully," said police spokesman Winfrid Wenzel.
Police have however stressed that the bomb was "safe for now", reassuring nearby residents that "there is no immediate danger".
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)
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