The action came as relatives and survivors marked the 20th anniversary of the bombing that killed four people and injured some 1,000 others.
"We have no greater responsibility than providing for the safety and security for our citizens, allies and partners. ... The use of improvised explosive devices ... threatens these interests by killing, injuring and intimidating citizens and political leaders around the world," Obama said in an accompanying statement.
"The terrorists and criminals responsible for these attacks are resilient, technologically adept and adaptable."
The policy calls for a "whole-of-government approach" to unearth plots involving IEDs.
Edward Smith, whose wife Monica was one of four people who died, told ABC News.com he couldn't continue to live in New York after her death but makes a trip to the city every February for a memorial.
"There were too many reminders. It was too much," Smith said.
Smith's wife was eight months pregnant with their first child and about to begin her maternity leave when terrorists detonated a truck bomb in the building's parking garage on Feb. 26, 1993.
Peter Goldmark, who had retired form his job at the Port Authority when the bombing occurred, said he had set up a task force to look into terrorist threats at the end of his time in office.
However, he said, his successor dismantled his antiterrorist initiatives that included shutting down parking at the center.
"One of the things we recommended and were going to do would have prevented the '93 bombings," Goldmark said.
He added his "heart went cold" when he heard about the bombing.