The working paper published and sponsored this month by the World Bank criticises local and foreign media for inflating the threat posed by Islamic schools and their educating potential "jihadists".
Madrasas are often accused of cultivating religious radicalism and inciting militancy. Pakistan's President Pervez Musharraf, a key ally of the United States in its "war on terror", has come under intense pressure to clamp down on these schools.
Pakistani officials have always maintained that very few madrasas are involved in activities that promote militancy, but Musharraf urged his nation on Saturday to curb misuse of the schools.
Pakistan madrasas once taught
many Afghanistan Taliban
The study also expressed concern at the US 9/11 Commission report into the attacks on New York and Washington in 2001, which said "millions of families" send their children to religious schools in Pakistan.
"Striking, yet unsubstantiated claims such as 'millions of families ... send their children to religious schools' are of particular concern given the emphasis on identifying and curbing potential sources of extremism," it said.
The report dispelled general perceptions that enrolment was on the rise saying: "We find no evidence of a dramatic increase in madrasa enrolment in recent years."
It said figures reported by international newspapers such as the Washington Post, saying there were 10% enrolment in madrasas.
"It is troubling that none of the reports and articles reviewed based their analysis on publicly available data or established statistical methodologies," it said.
"We find no evidence
of a dramatic increase in madrasa enrolment in recent years"
World Bank study
The research, conducted by Jishu Das of the World Bank, Asim Ijaz Khawaja and Tristan Zajonc of Harvard University and Tahir Andrabil of Pomona College, said "madrasas account for less than 1% of all enrolment in the country".
"The educational landscape in Pakistan has changed substantially in the last decade," it said. "But this is due to an explosion of private schools, an important fact that has been left out of the debate on Pakistani education."
Schools previously popular
It said during the religious-based resistance to the invasion of Afghanistan by the Soviets in 1979, madrasas became popular in the northwestern and southwestern Pakistan.
Many of these students came from Afghanistan and some of them formed the Taliban movement, which rose to power in 1996 but was ousted by the US in late 2001 after the September 11 attacks on the US.
The report said the Pakistani districts where madrasa enrolment was relatively high were in the "Pashtun belt" near the Afghan border while in the rest of the country enrolment was very low.
But, "even in the districts that border Afghanistan where madrasa enrolment is highest in the country, it is less than 7.5% of all enrolled children", the report said.