The bomb was unearthed in the northern port city during road works last week. It was found near a petrol station.
"The first phase, the defusal was a total success," said regional security chief Apostolos Tzitzikostas at midday, less than an hour after the demining team started operations.
"The bomb's removal from the site begins," Tzitzikostas added, explaining that the bomb would be taken to an army firing range nearby.
Some 70,000 people were evacuated within a 1.9-kilometre (1.1-mile) radius of the site, affecting three working-class neighbourhoods west of the city centre.
Evacuation is "obligatory", Tzitzikostas told reporters Friday. The evacuation order remains in effect until the end of all operations, Tzitzikostas said Sunday.
The operation is unprecedented in Greece, "where a bomb of this size has never been found in an area this densely populated," Tzitzikostas said.
Many chose to do so "because they are scared of thieves," he said.
Some of those evacuated complained. A woman in her eighties muttered as she was taken away: "There's no reason to be scared, if the bomb had to go off it would have done so already."
Most of the buses brought for evacuation remained empty however as many people left on their own. Some 400 refugees in a nearby camp were also bussed to safer areas.
The army however has not confirmed or denied the report.
Seven decades after the end of World War II, unexploded bombs from the conflict are still being found around the globe.
On January 23, dozens of people were evacuated after a bomb was found near a Hong Kong university, while three days before that Britain's navy disposed of a suspected wartime bomb found close to the parliament in London.
In the German city of Augsburg, 54,000 people had an unwelcome Christmas surprise on December 25 when they had to leave their homes while authorities dealt with a bomb dropped by Britain during the war.
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