The Islamic State had claimed responsibility for the attack.
Security measures were boosted after a May 31 truck bomb attack near the German embassy in the diplomatic quarter that killed at least 150 people and wounded about 400 others.
The interior ministry said the attacker blew himself up near the gate of the National Directorate of Security.
The blast follows an attack fended off during an hours-long gun battle a week ago at a Kabul training facility of the agency.
According to Tolo News, the attack occurred at about 8am in Shash Darak area near Abdulhaq Squar targeting the office.
Afghan security forces remove a destroyed vehicle on Monday.
However, no group including the Taliban has yet claimed responsibility for the attack. The Western-backed government there has been struggling to fend off militants since the withdrawal of most North Atlantic Treaty Organisation troops in 2014.
On October 20, suicide bombers attacked two Shi'ite mosque in the city, killing more than 72 people. Islamabad denies the allegations.