A committee of experts looked at all the possible excuses--biological differences in ability, hormonal influences, child-rearing demands and even differences in ambition--and found no good explanation for why women are being locked out.
"Compared with men, women faculty members are generally paid less and promoted more slowly, receive fewer honors, and hold fewer leadership positions," the academies said in a statement.
"These discrepancies do not appear to be based on productivity, the significance of their work or any other performance measures."
Female minorities fare the worst, the study found. The expert panel said the discrepancies are costing the country many talented leaders and researchers, and recommended immediate and far-reaching changes to alter the balance.
"We found no significant biological differences between men and women in science, engineering and mathematics that could account for the lower representation of women in academic faculty and scientific leadership positions," said Donna Shalala, president of the University of Miami and head of the committee that wrote the report.
The study was compiled by all the National Academies--the National Academy of Sciences, National Academy of Engineering, National Research Council and the Institute of Medicine--which advise Congress, the federal government and various institutions.
"It is not a lack of talent but an unintended bias...that is locking women out," Shalala, a former secretary of the U.S. Department of Health and Human Services, told a briefing. "Fundamental changes in the culture and opportunities at America's research universities are urgently needed."
"A substantial body of evidence establishes that most people--men and women--hold implicit biases," the report reads.
And it noted that the problem is not restricted to academia, or even to science.
"The underrepresentation of women and minorities in science and engineering faculties stems from a number of issues that are firmly rooted in our society's traditions and culture," the report reads.
Many arguments have been made to explain why women do not excel in math and science--that they are not as good as men in mathematical ability, that female brain structures are different or that hormones affect performance.
Lawrence Summers resigned as Harvard University president after he made widely disparaged remarks in 2005 suggesting that women were biologically less able in math and science, and that women chose to pay more attention to their families and thus failed to put in enough effort to succeed at work.
The experts looked at many different studies on the issue.
"The committee found no sound evidence to support these myths and often good evidence to the contrary," said Ana Mari Cauce, executive vice provost at the University of Washington in Seattle.
"In fact, female performance in high school mathematics now matches that of males. If biology were the basis of that, we've seen some major evolution in the past decades."
Urgent change is needed, said Cauce, if the United States wants to compete internationally in science.
"This is about more excellence. This is not about changing the bar or lowering the bar," Cauce said.
Trustees, university presidents and provosts need to make it clear from the top down that recruiting and promoting women is a priority, the report said.