Mohsin Naqvi said a bomber was planning to attack the district courthouse but was unable to get inside.
Naqvi said authorities would prioritise identifying the bomber, and that those involved would be brought to justice.
Pakistani Prime Minister Shehbaz Sharif has alleged that extremist groups "actively backed by India" were involved.
A spokesperson for the Indian government denied what they described as "baseless and unfounded allegations".
In a statement, Sharif said that "terrorist attacks on unarmed citizens of Pakistan by India's terrorist proxies are condemnable".
Jumaat Ul Ahrar, a splinter group of the Pakistani Taliban (TTP), has claimed responsibility, according to local media. But two local journalists have told the BBC that the TTP's central leadership has sent messages to them saying it has no link to the explosion.
Suicide blasts in Islamabad have been rare in recent years. Footage from the scene on Tuesday showed the remains of a burnt-out car and a police cordon in place.
The 27 people injured are receiving medical treatment, Naqvi said.
He added that the attacker detonated the bomb close to a police car after waiting for up to 15 minutes.
Footage of the aftermath showed plumes of smoke rising from a charred vehicle behind a security barrier. The incident occurred at 12:39 local time (07:39 GMT).
Pakistani President Asif Ali Zardari said he "strongly condemned the suicide blast".
A lawyer who said he was parking his car outside the court at the time described hearing a "loud bang".
Rustam Malik told AFP news agency "it was complete chaos".
"Lawyers and people were running inside the complex," he added. "I saw two dead bodies lying on the gate and several cars were on fire."Police cordoned off an area close to a district court in Islamabad after the blast
In a separate incident on Monday, a car exploded in India's capital Delhi, killing eight people and injuring a number of others.
The Indian government has not called the incident a terror attack, although the case has been referred to the country's anti-terror body.
Indian Prime Minister Narendra Modi said following the attack: "The conspirators behind this heinous act will not be spared. All those responsible will be brought to justice, no matter how deep the conspiracy runs."
There is, however, no official word yet on what led to the blast.
The last time Pakistan's capital was targeted by a suicide bombing was three years ago when a police officer was killed and several others injured.
There have been suicide attacks in other parts of the country in the years since but not in Islamabad.
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