No evidence of any gunman was found despite a room-to-room search by police.
Authorities lifted a lockdown for the entire Ivy League campus late Monday afternoon, according to the university's Twitter feed.
"New Haven is safe," said New Haven Police Chief Dean Esserman. "The Yale campus is safe."
A 911 call was received at 9:48 a.m. from a man at a pay phone about a mile from the campus who said his roommate was on the way to the university to shoot people, said Officer David Hartman, a New Haven Police spokesman.
"Though it is starting to tilt in the direction of an innocent mistake, it started with a purposeful and malicious call," Esserman said, vowing to track down and arrest the person who made the call.
The hunt, which came as the school was on November break, was stymied by students who had stayed behind and were afraid to open their doors, police said.
Police later received reports from witnesses who reported seeing someone with a gun, Hartman said. But he said it was possible they had simply seen officers responding to the initial call.
There was nothing specific about the threat, he said, and the call lasted only seconds. There were no reports of shots fired or anyone injured.
Police blocked off several streets near the university's Old Campus, in the heart of New Haven, where they were concentrating their search. Several local schools also were placed in lockdown. Police in tactical gear entered several campus buildings, and a helicopter hovered over the area. Pedestrian traffic in the normally bustling area was sparse, with cold and windy weather keeping many people inside.
The response included several police departments, the FBI and other federal agencies, Hartman said. Authorities were conducting a room-by-room search of buildings, he said.
Yale advised students and staff members to shelter in place. The school also issued an advisory asking people off campus to stay away from the area. The shelter advisory was lifted for most of the campus by 3:30 p.m.
Many students and staff members left campus for the Thanksgiving holiday following Saturday's traditional football game against Harvard.
But many others were still in their dorm rooms, Hartman said. Police were having difficulty gaining access to some rooms because those locked inside were not convinced they were dealing with law enforcement, he said. Most rooms don't have peepholes.
Yale sent out an email telling community members that officers would be slipping a Yale ID under the door or using keys to gain access.
Undergraduate classes are set to resume Dec. 2
Yale has been the target of violence in the past. In May 2003, a bomb damaged an empty classroom and adjacent reading room at the law school.
A Yale professor, David J. Gelernter, was seriously injured in 1993, when a mail bomb mailed by Theodore Kaczynski, the man known as the Unabomber, exploded in his campus office.
Monday' search came several weeks after a scare on another Connecticut campus.
Central Connecticut State University was in lockdown for several hours Nov. 4 after reports by witnesses of a masked man carrying a gun or sword.
Police arrested a student, David Kyem, who said he had been wearing a ninja-like Halloween costume and meant no harm. He faces charges including breach of peace.