The move by Chaudhry will pave the way for the two commissions to begin their work.
Though the government formed the commissions and appointed two apex court judges to head them, the judges refused to take up the responsibility on the ground that the Chief Justice had not been consulted.
Chief Justice Chaudhry yesterday approved the government's requests for Justices Javed Iqbal and Saqib Nisar to head the separate inquiry commissions.
Iqbal will head the probe into bin Laden's presence in Pakistan and the US operation in the garrison city of Abbottabad that killed the al-Qaeda leader on May 2.
Nisar will head the inquiry into the abduction and murder of Shahzad, who was killed days after he alleged in an article that al-Qaeda had infiltrated the Pakistan Navy.
The government had approached the apex court to request the Chief Justice to appoint the judges to head the inquiry commissions.
The request was put up before the Chief Justice and he gave his consent by nominating the two judges as requested by the government.
Rights groups, civil society organisations and defence experts have criticised the delay in the formation of the two commissions.