The rockets and their launchers were hidden near a building site in the area, which is also where the Pakistani president's official residence and other official government buildings are located.
A mobile phone was attached by wires to both launchers, apparently for use as a remote trigger. They were reportedly found by a construction worker.
Police and the army cordoned off nearby roads from traffic and senior security officials told Reuters news agency that they had detained several people for questioning.
The alert follows an explosion on Wednesday in the city of Rawalpindi, south of Islamabad, about two kilometres from Musharraf's army residence.
No one was hurt in the blast.
Pervez Musharraf, the Pakistani president, has just returned from talks in Washington with George Bush, the US president.
The army general seized power in a coup seven years ago and is a main ally of the United States in its so-called war on terror.
After the 11 September 2001 attacks, the US invaded Pakistan's neighbour, Afghanistan, to remove the Taliban regime.
Musharraf has survived two assassination attempts, most notably in December 2003 when two suicide bombers rammed his presidential convoy, killing 17 people.