Opposition deputies began shouting "Down with dictatorships," "Go, Musharraf, go!" and "No, Musharraf, no!" as soon as the president was invited to speak.
Other deputies walked out of the chamber, and there was more noise, too, from Musharraf's supporters, who banged their benches in a sign of approval of his speech.
Musharraf called on deputies to wage "jihad," or holy struggle, against extremism.
He said Pakistan must counter its image as an extremist society and a source of terrorism in Afghanistan, and he vowed to hunt down Al-Qaeda and Taliban militants thought to be orchestrating attacks there from Pakistan's tribal regions.
Musharraf also said Pakistan must move to resolve its decades-old dispute with India over Kashmir, following a landmark agreement with
India last month to resume talks on the issue.
He also said Pakistan would not allow any proliferation of nuclear weapons. But at the same time he reiterated a vow to strengthen Pakistan's nuclear and missile defense program.
Pakistan's constitution requires the president to address parliament every year, but Musharraf had been prevented from doing so by a stand-off with the opposition.
A deal with a hard-line Islamic alliance last month ended that stalemate.
"Musharraf called on deputies to wage 'jihad,' or holy struggle, against extremism."
Under the deal, Musharraf agreed to step down as army chief at the end of this year in return for support from Islamist hard-liners.
But today's rowdy session showed Musharraf has failed to win total support from the Islamists, who are angry at his support for the U.S.-led war on terror.
There were also complaints that several opposition members had been unable to attend today's session because authorities diverted their plane from Islamabad.
Airline officials said two planes were diverted because of a hoax bomb warning at Islamabad airport.