In an interview with a US television network on Friday, one day after Zawahiri urged the Pakistani military to oust the country's president in an audio tape first aired on al-Jazeera, Musharraf said the threat meant little.
"Now as far as if he's taunting me well, I would like to say that I am going to eliminate all of them," Musharraf said.
"I mean, Zawahiri is on the run. For heaven's sake, its just one tape. Let's not get excited," he said.
The US intelligence meanwhile has described the tape attributed to Zawahiri as "probably genuine."
In the tape, Zawahiri called on Pakistan's military to "not obey orders" and overthrow Musharraf's government, calling it a "traitor government."
The tape came amid an intensified Pakistani military offensive against suspected Taliban and al-Qaida fighters along the country's northern border with Afghanistan.