An audio recording purportedly made by senior al-Qaeda figure Ayman al-Zawahri has been broadcast by the pan-Arab television station, al-Jazeera.
Ayman al-Zawahri (left) is regarded as al-Qaeda's ideologue
The message urges Pakistan's Muslims to overthrow President Pervez Musharraf.
Analysts say the voice sounds like previous tapes of Mr Zawahri but it is unclear when the recording was made.
Pakistani soldiers have been attacking suspected al-Qaeda sympathisers whom officials believed had possibly been sheltering Mr Zawahri.
"I call on Muslims in Pakistan to get rid of their government which is working for Americans," said the taped voice.
In particular, it urged soldiers in Pakistan's army to "disobey orders" and carry out a coup d'etat against Gen Musharraf.
Earlier on Thursday, fighters resisting the Pakistani army ignored a deadline to surrender themselves along with several soldiers they have taken hostage.
The BBC correspondent in the region says the Pakistani army is pinning its hopes on further talks with the area's tribal elders, who are accused of sheltering the militants.
The army seems wary of launching a fresh offensive against the heavily-armed fighters, having suffered severe losses in the last fortnight.
Pakistan's army has been waging an offensive along the country's western border with Afghanistan - traditionally a stronghold of deeply conservative Pashtun tribes.
The intensity of the fighting in the South Waziristan region prompted speculation that the tribesmen were protecting a "high-value" al-Qaeda target.
But with no sign of Mr Zawahri among those killed or captured, Pakistani officials later conceded the claim may just have been "guesswork".
Other reports suggested Mr Zawahri - if indeed he was there - may have fled the fighting through a network of underground tunnels.
The army operation coincided with an US military sweep in neighbouring Afghanistan, as US marines tried to seal the rugged, mountainous Pakistani border to net any suspects attempting escape.
Gen Musharraf faces strong domestic opposition to his support for the US-led "war on terror" and survived two recent assassination attempts, later blamed on al-Qaeda militants.