The threat was called in via telephone at 8.30am on Monday for Sankt Paulsgatan on Södermalm. All 165 employees at the Swedish Standards Institute (SIS) were told to leave the building, as were employees at nearby offices and buildings.
The area, which is right by the corner of the Oliver Twist pub, was cordoned off by police soon after.
Police have launched an investigation into aggravated illegal threats (grovt olaga hot), reported the TT news agency.
"We have no idea what this is all about, everyone is equally perplexed," Lovisa Krebs at SIS told TT. She added that she was unsure if the threat was specifically directed at the office. SIS works with developing standards in domains including constructions, healthcare, and engineering.
Employees headed to cafés in the area while awaiting further instructions.