The NSC bill has already been passed by the two houses of Pakistani parliament.
Officials said it was forwarded to Musharraf, who approved the bill on Monday.
The new law calls for establishing a 13-member National Security Council made up of military chiefs and nine civilian leaders to shape policy on national security issues.
Musharraf, who is also the country's army chief, will head the council, which he says will only be a "consultative" body.
But critics have charged the council will give military brass a say in the policies of a democratically-elected government.
Musharraf, who seized power in a military coup in October 1999, held elections in October 2002.
The main opposition Pakistan People's Party of former prime minister Benazir Bhutto has vowed it would overturn the new law when it gains the parliamentary strength to do so.
Pakistan has been ruled by generals for almost half of its 57-year history.