Pakistan will suffer from sanctions and "they may even start bombing our tribal areas", General Musharraf told local newspaper editors late on Thursday, according to Friday’s Dawn daily.
He did not specify who would drop bombs on Pakistan but was understood to be referring to the United States. US troops are combing the Afghanistan-Pakistan border in their two-year hunt for al-Qaida and Taliban fighters and al-Qaida chief Usama bin Ladin.
"If we don't control the tribal areas and they start bombing your tribal areas, what will we do? Let us not be under any illusion," the Nation newspaper quoted Musharraf saying.
Al-Qaida and Taliban fighters are believed to be using bases in Pakistani tribal areas along the porous border to wage a guerrilla campaign against aid workers and troops inside Afghanistan. Eighteen fighters were captured and eight killed by Pakistani troops near the border on 2 October.
Musharraf issued the warning in the midst of an intensified crackdown on alleged Islamic extremists, targeting already-outlawed groups which had reemerged under new names.
Violence by religious groups has
brought troops on to the streets
Authorities are also swooping on suspected Taliban sympathisers among illegal Afghan immigrants in the southwest border province of Baluchistan.
Since Saturday, Musharraf has banned six groups and placed one under surveillance, accusing them of promoting extremism and religious intolerance.
Police in Baluchistan have arrested 500 Afghan illegal immigrants and begun deporting them.
Musharraf said the world had started suspecting he and the government were supporting “extremists and terrorists”.
Bombs would be dropped and sanctions slapped on Pakistan "if this perception is not removed urgently", Dawn quoted him saying.
"This is one area which will drown us."
Scores of Islamist groups sprouted in Pakistan in the wake of the 1979-1989 war to oust Soviet invaders from neighbouring Afghanistan and since the start of a guerrilla insurgency in disputed Kashmir against Indian forces in 1989.