The loud blast erupted close to the NATO's International Security Assistance Force (ISAF) headquarters and in an area of the capital that houses many embassies and international institutions.
ISAF confirmed that the blast occurred outside their headquarters, while the US embassy sounded its emergency "duck and cover" sirens to warn employees to seek shelter.
"It was an accident, not an enemy act," Lutfullah Mashal, an official from the National Directorate of Security (NDS) intelligence agency, told AFP.
An NDS spokesman told local television that the blast happened in an NDS depot that contained explosives, unexploded bombs and suicide vests seized from insurgents.
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The interior ministry also confirmed the explosion was an accident.
The blast came the day after a Taliban suicide bomber detonated an explosives-laden vehicle near a NATO military convoy entering Kabul airport, killing himself but causing no other deaths or injuries.
The airport houses another NATO base as well as operating civilian flights to cities including Dubai, New Delhi and Istanbul. Flights were delayed only briefly after the bomb exploded.
Kabul has seen a recent drop in insurgent attacks after a series of high-profile strikes earlier this year, with the NDS claiming to have foiled several plots to launch complex strikes involving truck bombs and suicide gunmen.
A series of attacks earlier this year targeted foreign compounds, the Supreme Court, the airport and the presidential palace in the city.