WASHINGTON — A special prosecutor has ended his four-year investigation into possible FBI misconduct in its probe of ties between Russia and Donald Trump’s 2016 campaign with withering criticism of the bureau but a meager court record that fell far short of the former president’s prediction he would uncover the “crime of the century.”

The report Monday from the special counsel, John Durham, represents the long-awaited culmination of an investigation that Mr. Trump and allies had claimed would expose massive wrongdoing by law enforcement and intelligence officials. Instead, Mr. Durham’s investigation delivered underwhelming results, with prosecutors securing a guilty plea from a little-known FBI employee but losing the only two criminal cases they took to trial.

The roughly 300-page report catalogs what Mr. Durham says were a series of missteps by the FBI and Justice Department as investigators undertook a politically explosive probe in the heat of the 2016 election into whether the Trump campaign was colluding with Russia to tip the outcome.

It criticized the FBI for opening a full-fledged investigation based on “raw, unanalyzed and uncorroborated intelligence,” saying the speed at which it did so was a departure from the norm. And it said investigators repeatedly relied on “confirmation bias,” ignoring or rationalizing away evidence that undercut their premise of a Trump-Russia conspiracy as they pushed the probe forward.

“Again, the FBI’s failure to critically analyze information that ran counter to the narrative of a Trump/Russia collusive relationship exhibited throughout Crossfire Hurricane is extremely troublesome,” the report said. “Crossfire Hurricane” was the FBI code name for its investigation.

The impact of Mr. Durham’s report, though harshly critical of the FBI, is likely blunted by Mr. Durham’s spotty prosecution record and by the fact that many of the seven-year-old episodes it cites were already examined in depth by the Justice Department’s inspector general.

The FBI has also long since announced dozens of corrective actions. Still, Mr. Durham’s findings are likely to amplify scrutiny of the FBI at a time when Mr. Trump is again seeking the White House as well as offer fresh fodder for congressional Republicans who have launched their own investigation into the purported “weaponization” of the FBI and Justice Department.

The FBI released a letter to Mr. Durham outlining changes it has made, including steps to ensure the accuracy of secretive surveillance applications to eavesdrop on suspected terrorists and spies. It also stressed that the report focused on prior leadership.

“Had those reforms been in place in 2016, the missteps identified in the report could have been prevented. This report reinforces the importance of ensuring the FBI continues to do its work with the rigor, objectivity, and professionalism the American people deserve and rightly expect,” the FBI said in a statement.

The former U.S. Attorney in Connecticut, Mr. Durham was appointed in 2019 by Mr. Trump’s attorney general, William Barr, soon after a special counsel, Robert Mueller, had completed his investigation into whether the 2016 Trump campaign had colluded with Russia to move the outcome of the election in his favor.

The Mueller investigation resulted in roughly three dozen criminal charges, including convictions of a half-dozen Trump associates, and concluded that Russia intervened on the Trump campaign’s behalf and that the campaign welcomed the help.

But Mr. Mueller’s team did not find that they actually conspired to sway the election, creating an opening for critics of the probe — including Mr. Barr himself — to complain that it had been launched without a proper basis.

The original Russia investigation was opened in July 2016 after the FBI learned from an Australian diplomat that a Trump campaign associate named George Papadopoulos had claimed to know of “dirt” that the Russians had on the Democratic candidate, Senator Clinton, in the form of hacked emails.

Yet disclosures over the following months laid bare flaws with the investigation, including errors and omissions in Justice Department applications to eavesdrop on a former Trump campaign aide, Carter Page, as well as the reliance by the FBI on a dossier of uncorroborated or discredited information compiled by an British ex-spy, Christopher Steele.

Mr. Durham’s team delved deeply into those mistakes, finding that investigators did not corroborate a “single substantive allegation” in the so-called Steele dossier and ignored or rationalized what it asserts was exculpatory information that Trump associates had provided to FBI confidential informants.

Mr. Durham’s mandate was to scrutinize government decisions, and identify possible misconduct, in the early days of the Trump-Russia probe. His appointment was cheered by Mr. Trump, who in a 2019 interview with Fox News said Mr. Durham was “supposed to be the smartest and the best.”

Mr. Trump and his supporters expressed hopes that it would expose a “deep state” conspiracy within the top echelons of the FBI and other agencies to derail Mr. Trump’s presidency and candidacy.

Mr. Durham and his team cast a broad net, interviewing top officials at the FBI, Justice Department and CIA. In his first year on the job, he traveled with Barr to Italy to meet with government officials as Trump himself asked the Australian prime minister and other leaders to help with the probe.

Weeks before his December 2020 resignation as attorney general, Mr. Barr appointed Mr. Durham as a Justice Department special counsel to ensure that he would continue his work in a Democratic administration.

The slow pace of the probe irked Mr. Trump, who berated Mr. Barr before he left office about the whereabouts of a report that would not be released for several more years. By the end of the Trump administration, only one criminal case had been brought, while the abrupt departure of Mr. Durham’s top deputy in the final months of Mr. Trump’s tenure raised questions about whether the team was in sync.

Despite expectations that Mr. Durham might charge senior government officials, his team produced only three prosecutions. A former FBI lawyer pleaded guilty to altering an email the FBI relied on in applying to eavesdrop on an ex-Trump campaign aide.

Two other defendants — a lawyer for the Clinton campaign and a Russian-American think tank analyst — were both acquitted on charges of lying to the FBI.