Norway has been on high alert since Thursday, when its intelligence service (PST) said it had "recently received information that a group of extremists from Syria may be planning a terrorist attack" in the country.
"Police have requested Avinor (Norway's state-owned airport operator) to ban flights over central Bergen," said Gustav Landro, chief of staff at theHordaland county police department.
"The reason is the increased threat situation we have had since Thursday," he added.
Police said the airspace ban applied only to smaller private and recreational flights over the centre of the city in western Norway.
Bergen's airport was not disrupted and was operating normally, police said.
On Saturday, authorities said they would check the ID of all travellers entering Norway until further notice.
Norway is not an EU member but is part of the Schengen area, which includes 26 European countries that have abolished passport and other types of border controls for people travelling within the group of nations.
At a press conference on Friday, Odd Reidar Humlegård, head of the police directorate, said any security incident was unlikely.
"But this time around, we will be more prepared than ever to handle the situation if it occurs," he added in an implicit reference to the massacre by right-wing extremist Anders Behring Breivik, who killed 77 people in July 2011, when police were heavily criticised for their slow reaction.
The threat is "non-specific" but "credible", according to PST chief Benedicte Bjørnland.
On Friday, the Oslo Jewish Museum in Norway announced it would remain closed to the public until Sunday.
There are concerns Norway's Jewish community could be targeted following the deadly attack on Brussels' Jewish Museum in May.
The suspected perpetrator is French-Algerian Mehdi Nemmouche, who spent more than a year fighting alongside jihadist militants in Syria.