Although officials sought Wednesday to downplay the seriousness of the threats, some security experts warned that such a break-in could potentially enable a serious attack on the Internet.
Stanford University, the National Center for Atmospheric Research, the San Diego Supercomputer Center and the University of Illinois' National Center for Supercomputing Applications were among the systems hit.
In a statement, the atmospheric center said its supercomputers were compromised, and parts of its networks have been taken offline indefinitely.
Also affected was TeraGrid, a government-funded effort to link together several supercomputers, including those at San Diego and NCSA, so scientists can better crunch data for weather forecasting, astronomy and medicine.
"There's been some unauthorized access, but it's not that anything has been damaged or taken over," said Catherine Foster of Argonne National Laboratory, home to TeraGrid's coordinator. "This seems to be part of an effort (by hackers) to gain merit badges."
Foster said some TeraGrid computers had to be taken offline while security upgrades were made, disrupting research. She said the attacks began in March and that all systems should be restored by week's end.
Mike Levine, scientific director at TeraGrid member Pittsburgh Supercomputing Center, said the TeraGrid sites performed no classified work so there are "no implications for national security."
But Peter Allor, director of intelligence with the Internet Security Systems' X-Force research unit, said universities and research institutions are prime targets for hacking because they have very powerful computers with plenty of Internet bandwidth.
He said those resources could be tapped to launch so-called denial-of-service attacks that can disrupt major Web sites and e-mail systems around the world, potentially bringing down the Net.
Investigations are continuing, and law enforcement authorities have been contacted. No one could specify how many institutions have been compromised, though officials describe the number as large.
By Anick Jesdanun