Matt Baggott said he was saddened after a car bomb claimed by the Real IRA exploded in Holywood, Co Down - minutes after security powers were transferred from London to Belfast.
A taxi driver was taken hostage in north Belfast and held for two hours before being forced to drive the device to Palace Barracks near where MI5 is based.
Most of the damage was confined to the perimeter of the base and there were no serious injuries.
Security personnel were evacuating the area when the device exploded and some of the 30 to 40 fleeing residents dived for cover to avoid shrapnel.
Mr Baggott said: "The threat is very severe and there are a significant minority of people who want to take us back to the past in the very worst sense that could bring."
One elderly man was slightly injured in the attack after he was walking nearby when the device exploded.
The Real IRA has been linked to a string of attacks against security forces and last year shot dead two soldiers at Massereene Army base in Co Antrim.
The devolution move was agreed in the Hillsborough Castle Agreement brokered in February between the Democratic Unionist Party (DUP) and Sinn Fein.
But while the development will bring a raft of new powers into the hands of Stormont politicians, responsibility for national security and related intelligence-gathering is not to be transferred.