FBI Counterintelligence Slips Amid Immigration Focus

The FBI’s counterintelligence squads have been severely depleted across the country, with many units operating 50% to 60% below full staffing, according to an exclusive NPR report published October 6, 2026. The shortfalls come as the bureau shifts resources toward immigration enforcement and violent crime—top political priorities of the Trump administration—even as the United States confronts heightened espionage and cyber threats from China, Russia, and Iran.

A Quiet Erosion of Capability

The staffing shortages are not the product of a direct order to dismantle counterintelligence work. Instead, they are a structural consequence of FBI leadership’s focus on other priorities. In many of the bureau’s 56 field offices, counterintelligence squads have only 50% to 60% of positions filled, and in multiple offices the number of squads doing such work has been cut in half.

According to five people familiar with the matter who spoke on condition of anonymity, field offices have pulled agents and analysts off counterintelligence and reassigned them to immigration and violent crime. Special agents in charge of field offices are not backfilling those vacancies, instead assigning new personnel to administration priority issues.

“It’s terrifying, honestly,” one of the people familiar with the matter told NPR. “Threats are growing and we’re facing it with less and less. Not a recipe for success.”

The shift has also been compounded by FBI Director Kash Patel’s push to relocate analysts out of the bureau’s Washington, D.C. headquarters and into the field. While some former officials see merit in that effort, the side effects have been significant: when counterintelligence-focused analysts moved to field offices, many were shifted off counterespionage work and toward violent crime and gang cases. The loss has made it harder to open new investigations and, when cases do proceed, harder to interpret evidence and set investigative direction.

A Broader Personnel Drain

The counterintelligence cuts are part of a wider manpower exodus at the bureau. According to two people familiar with the matter, the FBI has lost more than 1,500 special agents since President Trump returned to office, and the agency is down more than 650 agents from January 2025 levels. Experienced agents and analysts have departed, taking institutional knowledge that is critical for complex, long-running counterintelligence cases, where building sources and cases can take years.

“When you lose that knowledge, you don’t just replace it with a brand new agent,” one source said. “You lose the experience and are starting from scratch. There’s a huge learning curve for this work.”

Some departures have been involuntary. Five special agents and a supervisor, all of whom worked Iranian counterintelligence threats, were dismissed days before the Trump administration launched its war on Iran, as The Independent has reported. They were among several special agents who worked on counterintelligence, including in New York, who were fired for having been involved in investigations of President Trump.

FBI Pushes Back

The bureau disputes the premise of the reporting. An FBI spokesperson called the account “false,” telling NPR: “The FBI maintains a robust counterintelligence operation across the enterprise.” The spokesperson said the bureau has expanded its counterintelligence task forces to more than 1,500 personnel, including personnel from partner agencies and state and local law enforcement, and defended its security work at recent major events including America’s 250th anniversary celebrations and the FIFA World Cup.

Addressing the sources, the spokesperson added: “Anonymous sources who criticize our counterintelligence capabilities are disconnected from reality.”

In recent congressional testimony, Patel said the FBI under his leadership had arrested more spies from Russia, China, Iran, and North Korea “than any FBI in history.” NPR said it could not independently verify that assertion. Experts note that arrest totals are not the most important measure of success in counterintelligence work, where the goal is often to disrupt and trace networks rather than to prosecute.

Why It Matters

Counterintelligence threats are silent by nature. Unlike a missed terrorist plot—which may end in a visible attack—a missed counterintelligence threat typically means the quiet, ongoing theft of government secrets or cutting-edge technology. That makes the true cost of a staffing shortfall difficult to measure publicly.

“I want to know things like how many people were kicked out of the country because of an investigation, or how many networks were completely exposed and halted,” said Emily Harding, a former CIA analyst and former deputy director of the Senate Intelligence Committee, who is now at the Center for Strategic and International Studies. “Sometimes the win is not the prosecution and the arrest. Sometimes the win is being able to trace a network all the way back to its source.”

Harding warned that the consequences of failure can be sweeping. “If the counterintelligence agents don’t manage to shut down the networks, you lose everything from intellectual property to economic standings in the world, so even something as bad as real government secrets that are highly classified,” she said.

The depleted units nonetheless continue to operate in a demanding environment. The U.S. remains mired in a war with Iran; China is described by American officials as waging a relentless campaign to steal U.S. secrets and technology; and Russia retains highly capable and aggressive intelligence services. In 2022, then-FBI Director Christopher Wray said the bureau had more than 2,000 investigations focused on Chinese efforts to steal U.S. information or technology and opened a new China-related case roughly every 12 hours.

The FBI has continued to notch counterintelligence wins. In May 2025, it arrested a former Defense Intelligence Agency computer specialist for trying to provide classified information to a foreign power; the employee pleaded guilty in August. In September 2026, the Justice Department charged five suspected Russian intelligence operatives for allegedly planning attacks in Europe and the U.S., including a purported assassination plot in Washington, D.C.

Critics of the director have been blunt. Robert Anderson, a former head of FBI counterintelligence, told The Bulwark that the situation is “a disaster,” adding, “Patel needs to wake up.” Frank Montoya Jr., a former FBI agent, told The Independent that “Patel is only paying lip service to the Chinese threat” and that the immigration focus has “put a disaster in play.” Commentary elsewhere has grown harsher, with Mother Jones calling the bureau a “rudderless ship” amid a string of leadership controversies.

What to Watch

The question now is whether the counterintelligence shortfall becomes visible in ways the public can measure—through prosecutions, expulsions of foreign operatives, or—more worryingly—through breaches that come to light only after the damage is done. Reporting has already flagged elevated security concerns across federal agencies, including broader fears tied to staff cuts at the FBI and Justice Department amid the Iran conflict.

For now, the debate hinges on competing claims: the FBI’s insistence that its capabilities remain robust, and the on-the-ground accounts of a mission quietly losing the people and resources it needs. With foreign threats intensifying and experienced personnel departing, the margin for error—in a discipline where failure is measured in stolen secrets rather than headlines—may be thinner than at any point in recent memory.