Musharraf's comments to the Financial Times came on the eve of a conference of rich nations in Geneva to discuss aid to Pakistan, where an estimated 3 million people have been left homeless by the October 8 quake that also struck India.
Musharraf defended his handling of the country's worst natural disaster saying the government "had done a good, if not a very good, job".
But he acknowledged that Islamic groups had stepped into an administrative vacuum in the days after the quake, providing relief and humanitarian assistance in Kashmir, a development that analysts say would bolster their legitimacy.
"I know they are doing a good job. But now we need to beat them to it. We need to provide better stuff," he told the newspaper. He added the government would act against the groups if they were found to be involved in activities other than welfare, such as drawing people towards militancy.