The changes require use of e-passports - paper passports that contain chips carrying biometric information - and expand use of US air marshals on international flights, the Department of Homeland Security said.
Some US lawmakers have been urging tighter restrictions on the waiver programme, which allows citizens from participating countries to enter the US without a visa for stays of 90 days or less.
Senator Dianne Feinstein, the top Democrat on the Senate Intelligence Committee, has criticised the programme as vulnerable to abuse, calling it the "the Achilles heel" of American efforts to stave off attacks on its soil.
The US intelligence community assessed in February this year that more than 20,000 foreign fighters, including at least 3400 Westerners, had traveled to the Syria-Iraq region since 2011.
Western fighters in Syria and Iraq have found some of their most willing recruits in Belgium, France and Britain, according to the International Center for the Study of Radicalization. All three participate in the visa waiver program, as do many European countries.
"The current global threat environment requires that we know more about those who travel to the United States. This includes those from countries for which we do not require a visa," Homeland Security Secretary Jeh Johnson said in a statement announcing the changes.
The new restrictions also require that participating countries use an international database to screen for lost and stolen passports, the department said.
It said the changes build on measures taken last year to require additional information on the application people in visa waiver countries provide to travel to the US.
The US Travel Association, an industry group, welcomed the passport security and air marshal changes but said it would evaluate other ones, including the development of passenger record databases and the screening of asylum-seekers.
"Though security should always be its first principle, it is well worth keeping in mind how the American economy and job creation both benefit when the (visa waiver programme) functions well," president Roger Dow said in a statement.
