WASHINGTON — An estimated 629,000 visitors to the United States — just over 1 percent of all travelers — remained in the country at the end of last year after overstaying their visas as students, workers or tourists, according to a report released on Monday by the Department of Homeland Security.

Although the figure represents a tiny portion of the estimated 50 million visitors to the country, Homeland Security officials say the failure of some people to leave when their visas lapse presents a national security risk. Two of the Sept. 11 hijackers, Satam al-Suqami and Nawaq Alhazmi, had overstayed their visas.

The report, just the second issued in the last 20 years despite being required annually by law, tracked overstays by citizens of countries that require a visa and of the three dozen or so countries, mostly in Europe, that participate in the visa-waiver program, which allows their citizens to visit the United States without a visa on trips of 90 days or less.

The highest rates of overstays were from countries outside the visa-waiver program. For example, 13 percent of the visitors from Afghanistan overstayed their visas, while nearly 11 percent of those from Iraq overstayed. The highest rates of overstays were from African countries. A quarter of all visitors from Burkina Faso and Djibouti overstayed their tourist or business visa.

European countries like France and Germany, which are exempt under the visa-waiver program, had lower overall rates of people overstaying their visas, less than 1 percent.

  

Homeland Security officials said the data captured in the report covered those arriving in the United States on planes or ships, even though more people enter the country by land.

The new report comes as the Trump administration accelerates its efforts to deport millions of undocumented immigrants and stop illegal immigration along the border with Mexico. President Trump’s plans include building a border wall to stem the flow of illegal immigration. But research shows that the majority of people in the country without permission are those who overstayed their visas rather than walking across a border.

The Department of Homeland Security has struggled to document visa overstays. A report released this month by its Office of Inspector General found that the agency could not account for all visa overstays in data it reports to Congress.

The inspector general’s report found that Immigration and Customs Enforcement, the agency responsible for investigating in-country visa overstays, had to piece together information from dozens of systems and databases, some of which were not integrated and did not electronically share information.

Officials said the department could not properly track visa overstays because there is no comprehensive biometric exit system at the country’s ports of departure to capture information on nonimmigrant visitors who leave the United States.

Without such an exit system, the department relies on third-party departure data, such as commercial carrier passenger or shipping manifests, to confirm that a visitor has left the country. However, these commercial sources occasionally provide incorrect departure or arrival status of visitors, the report said.

After the attacks of Sept. 11, 2001, an entry and exit tracking system was considered a vital national security and counterterrorism tool, and the 9/11 Commission recommended that the Department of Homeland Security introduce a system “as soon as possible.”

Since then, the federal government has spent millions of dollars on the effort, although until the release of the first report last year, officials could only roughly estimate the number of people who were in the United States illegally after overstaying visas. An executive order signed by Mr. Trump calls for the Department of Homeland Security to speed up efforts to create a biometric exit system.

Without such a system, lawmakers and Homeland Security officials fear that terrorists could exploit weaknesses in the visa program, including its inability to accurately track people who overstay.