Rahim Wardak told The Associated Press he received intelligence that Osama bin Laden's terror group is regrouping and intends to bring Iraq-style bloodshed to Afghanistan.
He also warned that the country could be in for several months of intense violence ahead of key legislative elections.
"We have gotten reports here and there that they have entered -- at least half a dozen of them," Wardak said. "The last report is that they came in just close to the time of the mosque attack."
The June 1 mosque blast killed 20 mourners at the funeral of a moderate cleric assassinated days earlier. That same day, a shoulder-launched, surface-to-air missile was fired at an American aircraft but missed.
On Monday, a suicide bomber drove up to a US military vehicle in Kandahar and detonated himself, wounding four American soldiers.
"It looks like there has been a regrouping of al-Qaeda and they may have changed their tactics not only to concentrate on Iraq but also on Afghanistan," Wardak said over tea at his wood-paneled office next to the heavily guarded presidential compound.
Authorities recovered the head of the mosque attacker and said he appeared to be of Middle Eastern descent. Wardak said initial indications are that the second suicide attacker also was an Arab.