In the original English edition of his book In the Line of Fire, launched in New York last month, Musharraf wrote that the US Central Intelligence Agency (CIA) made the payments after Pakistan handed over more than 350 prisoners.
"Those who habitually accuse us of not doing enough in the war on terror should simply ask the CIA how much prize money it has paid to the government of Pakistan," the military ruler said in the English version.
He said in his memoirs that Pakistan has captured 689 al-Qaeda suspects, including the alleged mastermind of the 9/11 attacks, Khalid Sheikh Mohammed.
But when Musharraf officially launched his autobiography in Urdu at the weekend - now called Sub seh Pehley Pakistan or Pakistan First - the claim was no longer there.
Musharraf's spokesman, Major-General Shaukat Sultan, said: "The president in an interview in the United States has already said that it was a mistake.
"He had said ... that thing had been published mistakenly, the government did not get any money," Sultan told AFP.
"That thing had been cleared [up] there and that is why it is not included in the Urdu edition."
But Musharraf's critics are sure to seize upon the significant deletion and allege that the bounty claim has been dropped as a matter of convenience.
Musharraf's support for the US "war on terror" has angered many Muslims in Pakistan. Any bounty claim in the Urdu book could have been seen by the Pakistani masses as a further proof of Musharraf's involvement in the US offensive.
Though a bestseller, Musharraf's book has generally been panned by the Pakistani media.
Several former Pakistani army generals have also criticised the president for giving out state secrets in the book, including the admission that Pakistani soldiers were involved in the Kargil war with neighbouring India.
Pakistan had never officially admitted its army's role in the conflict in 1999, which brought the two neighbours close to nuclear war.