WASHINGTON — Special counsel Robert Mueller's criminal investigation may be over, but the FBI's efforts to assess and counter Russian efforts to influence the U.S. political system — including the Trump administration — is continuing, current and former U.S. officials say.

The FBI and other intelligence agencies are pursuing a counterintelligence effort to thwart Russian influence operations in the U.S. and stymie an anticipated Russian effort to interfere in the 2020 election, the officials tell NBC News.

As part of that mission, analysts will continue to drill down on exactly how the Russians interfered in the 2016 election, whether any Americans helped them unwittingly, and whether any American continues to be compromised by Russia, experts say.

These are different questions than whether crimes were committed, which is what Mueller explored in his 448-page report. Mueller's report is silent on some of the key counterintelligence issues raised in his probe. It doesn't mention, for example, the counterintelligence investigation the FBI opened into the president — an inquiry former acting director Andrew McCabe said was designed to examine whether he was compromised by Russia. Nor does the report cite the counterintelligence briefing the Trump campaign is said to have received from the FBI, warning that Russia and other adversaries would seek to infiltrate the campaign.

"The fact that it's not present in the report tells me the ball is now and remains in the court of the FBI and the intelligence community," said Frank Figliuzzi, an NBC News contributor and former head of counterintelligence at the FBI.

It's unclear whether the counterintelligence investigation into Trump remains open. An FBI spokeswoman declined to comment.

Counterintelligence is also an issue the House Intelligence Committee will explore, said Rep. Adam Schiff, D-Calif., its chairman. The committee has requested an intelligence briefing on the Mueller investigation but has yet to receive a response, according to a congressional source.

"That's very important for our committee as well as the Financial Services Committee to make sure there's no financial leverage or other leverage that the Russians or the Gulf or anyone else have over the president of the United States," Schiff told MSNBC's Rachel Maddow Thursday.

In explaining his prosecution decisions, Mueller's report explores how a Russian intelligence operation sought to help Donald Trump get elected and how the Russian government later tried to influence his transition team and nascent administration. Mueller found no provable criminal conspiracy in those interactions.

But the report conspicuously avoids making an assessment about whether any of that conduct harmed national security. It scarcely mentions counterintelligence, and it doesn't say whether Mueller looked for financial ties between Trump and Russians or determined whether Russia has any leverage over the president or any member of his team.

In the one short section devoted to counterintelligence, the Mueller report makes clear that the issue of thwarting Russian influence went beyond the criminal probe.

For the last year, FBI counterintelligence analysts who were not working on the criminal investigation were embedded in Mueller's office, sending written summaries of foreign intelligence and counterintelligence to FBI headquarters and relevant field offices, the report says.

"From its inception, the office recognized that its investigation could identify foreign intelligence and counterintelligence information relevant to the FBI's broader national security mission," the report says.

Much of that information is not contained in the report, which was designed to summarize prosecution decisions. Left unsaid is that much of that information is also classified.

The sort of information that might have been included in those summaries — and which does not appear in the redacted report — might include details about Vladimir Putin’s role in the election interference operation, or the relationship between Russian intelligence and the St. Petersburg troll farm that manipulated U.S. social media.

"In fairness to Mueller, they were operating under rules built for a traditional criminal investigation," said Joshua Geltzer, a former senior attorney at the National Security Council under Presidents Obama and Trump.

"Those regulations had at least a somewhat different paradigm in mind. Counterintelligence investigations are by their nature sensitive and classified. It's not clear that there is much more that could or should be said publicly. But I do think the question of whether there are folks acting in ways contrary to our national interest is at least as important as the question of who is charged with a crime."

In a New York Times opinion piece Friday, Geltzer and Ryan Goodman, editor of the blog Just Security, call counterintelligence "the missing piece of the Mueller report."

"President Trump may claim 'exoneration' on a narrowly defined criminal coordination charge. But a counterintelligence investigation can yield something even more important: an intelligence assessment of how likely it is that someone — in this case, the president — is acting, wittingly or unwittingly, under the influence of or in collaboration with a foreign power," they write. "Was Donald Trump a knowing or unknowing Russian asset, used in some capacity to undermine our democracy and national security?"

A person on Trump's legal team, who declined to be identified because he was not authorized to talk to reporters, told NBC News that it was ridiculous to suggest that Trump is compromised by Russia after Mueller cleared him of conspiracy.

But the Mueller report seems to keep that question in play by explicitly stating that the Trump campaign and the Russian government had a shared interest.

"The investigation established that the Russian government perceived it would benefit from a Trump presidency and worked to secure that outcome, and that the campaign expected it would benefit electorally from information stolen and released through Russian efforts," the report says.

After the election, the report says, "Russian government officials and prominent Russian businessmen began trying to make inroads into the new administration. The most senior levels of the Russian government encouraged these efforts."

And members of the incoming Trump administration, including Mike Flynn and Jared Kushner, greeted the efforts with open arms, the report shows. Trump, for his part, continually expressed his desire to improve relations with Russia, and he said he would examine lifting certain sanctions.

Geltzer and other foreign policy experts have long said that Trump's favorable view of Russian President Vladimir Putin is so out of step with his own party, and seems so contrary to American interests, that it raises counterintelligence questions. When Trump proclaimed during last year's Helsinki summit he accepted Putin's claim that the Russians didn't meddle in the 2016 election, those questions deepened, Geltzer said.

These are not criminal questions that can be resolved in a court of law, experts say.

"Often in the worlds of intelligence it's about shades of gray that don't approach certainty," Geltzer said.

As part of its counterintelligence mission, the FBI makes assessments, including assessments about whether a particular American is acting as an agent of a foreign power, wittingly or not.

The next step is mitigation, which usually happens secretly. A foreigner can be placed under surveillance, or deported. A U.S. government official can be deprived of her security clearance or fired.

"I have been involved in cases where the objective was to determine whether a government official was playing for the other side or unwittingly duped or co-opted," Figliuzzi said. "The objective is to neutralize — detect, deter and defeat the threat."

But, Figliuzzi said, "deterring it and defeating it becomes problematic if it's the president of the U.S."