The blasts happened about 15 minutes apart, and in different districts of Lahore.
The first tore the facade of the Federal Investigation Agency (FIA) office, a seven-storey building.
While al-Qaeda-linked fighters in Iraq have regularly used vehicles to launch massive attacks on buildings, such damage has rarely been inflicted on a government building in Pakistan.
Azhar Hasan Nadeem, the provincial police chief, said it was not yet clear if al-Qaeda was involved in the attack.
"Of course they have a huge organisation, and they have a very vast network, but it would be premature to pinpoint exactly as to which particular organisation is responsible," he said.
In Lahore, Malik Mohammed Iqbal, a police chief, said that an explosives-laden vehicle managed to penetrate security, drive into a parking lot and detonate close to the FIA building.
The building houses part of the federal police's anti-terrorism unit - destroying offices on the lower floors and blowing out the walls around a stairwell.
Footage from a surveillance camera shown on private television showed a small truck running over a guard and speeding through the gate seconds before the blast.
The spike in violence across the country has prompted a number of Pakistanis to question Musharraf's approach to countering al-Qaida and the Taliban.
Musharraf's opponents say punitive military action has only fuelled the violence.