After waiting for more than three hours, passengers who were ordered to leave two sections of terminal five were allowed back to their gates at around 2pm.
The areas were evacuated on Tuesday morning following reports of fears that luggage in a plane contained a bomb.
"We received the threat at approximately 8:50 this morning and took immediate measures," Lars Byström from Stockholm police told The Local.
"A lot of people are confused about what is going on. It appears that flights are being delayed," said The Local's Paul Rapacioli who was at the airport soon after the threat emerged.
Passengers from his scheduled flight to Oslo were moved to another part of the airport but following "a bit of chaos" during the move, he reported that the mood soon became "pretty calm", with Swedes and international passengers waiting patiently for fresh information.
By mid-afternoon he reported "the cordon has been lifted and passengers are being allowed back into the gate area that was evacuated".
Passengers leaving terminal five on Tuesday. Photo: The Local
One passenger told Sweden's Aftonbladet newspaper that a pilot gave a message over a radio that there was a bomb threat against the plane circulating beside it. He said that the passengers had been told to get off and return to their gate.
"Some gates are blocked off while the police investigate," Ulf Wallin, a press officer for Swedavia which operates the airport told TT.
Another passenger told public broadcaster Sveriges Radio that police had evacuated a plane headed for Copenhagen following a bomb threat.
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Other unconfirmed reports said that police had taken a suspect into custody following a threat to an aircraft.
Arlanda is Sweden's largest airport and acts as an important hub for the Stockholm region and Scandinavia. It operates flights to 172 global destinations.
Terminal five after passengers were cleared from the area. Photo: The Local