The newspaper said officials at both schools had confirmed that Stephen LeMenager, Princeton's associate dean and director of admission, had repeatedly entered the Yale Web site.
Princeton has apologized for the intrusion, but Yale didn't seem ready to shrug off the matter.
Yale officials have notified the FBI about 18 unauthorized log-ins to the Web site that were traced back to computers at Princeton, including computers in the admissions office.
"We're assessing the information to see if there is a federal violation," FBI spokeswoman Lisa Bull said.
Marilyn Marks, a spokeswoman for Princeton, said LeMenager has been placed on paid administrative leave pending the outcome of an investigation into the matter.
LeMenager said the school checked the site simply to see how secure it was. Princeton gained access using information from students who had applied to both schools.
"It was really an innocent way for us to check out the security," LeMenager told the Yale Daily News, which broke the story in its online edition.
"That was our main concern of having an online notification system, that it would be susceptible to people who had that information — parents, guidance counselors, and admissions officers at other schools."
Attempts to reach LeMenager were unsuccessful. A telephone message left for an S.E. LeMenager in Pennington, N.J., the only LeMenager listed for the area, was not returned.
"The actions reported today by the Yale Daily News represent a serious lapse of judgment by at least one member of our admissions staff," Marks said. "The improper use of information provided to the university in good faith may have affected the ability of students to obtain information about their admission to Yale, something we deeply regret."
Yale said Princeton's actions violated the privacy of the students.
"We have therefore notified appropriate law enforcement authorities as well as the applicants whose Web locations were accessed," said Dorothy K. Robinson, Yale vice president and general counsel.
The Web site was activated in the spring so that undergraduate applicants could find out if they got into Yale. Applicants could access the site by using their Social Security numbers and birthdates. The site included links to admissions information and personal data about the students.
This was the first year Yale used the Web site, which proved to be popular with students. The day it went online in April, more than 9,700 applicants had logged in, including 1,190 of the nearly 1,500 students who were admitted.
If a student was admitted, the site flashed fireworks and a congratulatory message. If the student did not get in, a message indicating that was displayed.
The site included a notice that only students, not parents or others, may access the site, and it warned that Yale would investigate and act on any unauthorized use.
According to Yale officials, Princeton admissions staffers accessed some applicants' files before the students themselves had seen them. When those students went to the site they weren't automatically directed to the screen indicating whether they were accepted, since that screen only comes up at first login.
One of the students whose account was improperly accessed, Scott Grzenczyk of St. Louis, told The Washington Post that he was expecting "an apology or something along those lines" from Princeton.
The 18-year-old high school senior was rejected by Yale. He plans to attend Princeton.