WASHINGTON — With America warming to new negotiations with Iran, a recent report by counterterrorism experts at West Point suggests that, between 2001 and 2005, Iran harbored Al Qaeda’s third-ranking official and director of military operations, and that he could still be operating there today.

The disclosures in last month’s report, “Al Qaeda’s (mis)Adventures in the Horn of Africa,” from the Combating Terrorism Center at West Point, are the first official government documents to acknowledge that Saif al-Adel, who is one of the FBI’s most wanted terrorists, was inside Iran. Based in part on captured documents that were funneled to the government’s Harmony Database, the new disclosures suggest that Iran was more complicit with Al Qaeda than the Bush administration has previously suggested.

Some examples in the report include:

• Following a roundup of Al Qaeda operatives in Iran in early 2002, the report says that, from inside Iran, Mr. Adel helped organize a truck bombing of the Jewish synagogue of Djerba, Tunisia.

• In a captured letter from June 2002 to a mysterious “Brother Mukhtar,” Mr. Adel describes heavy losses sustained by Al Qaeda in Afghanistan and criticizes Osama bin Laden’s strategic leadership, which implies that he was still involved in Al Qaeda’s decision-making process.

• American and Saudi intelligence sources confirm that in 2003, Mr. Adel was in touch with Al Qaeda cells inside Saudi Arabia that had plotted a series of attacks on American targets.

• In December 2003, Mr. Adel began contributing to a magazine specializing in military matters produced by Al Qaeda known as Mu’askar al-Battar.

The New York Sun first reported that American intelligence officials believed that Mr. Adel resided in Iran in 2004, but American officials have only said on the record that they believe Al Qaeda operatives have traveled through and reside in Iran.

Within the intelligence community, it has remained an open question as to whether Mr. Adel was operating with the complicity of the Iranian regime. In 2005, Mr. Adel himself wrote that 80% of his organization was arrested by Iranian authorities in the first months of 2002. But in 2003, some intelligence and senior officials in the Bush administration believed Mr. Adel was still running operations for Al Qaeda under a lavish “house arrest” in Lazivan outside of Tehran, and in May and June of that year, American and Iranian diplomats discussed a possible swap of prisoners: Al Qaeda operatives for members of the People’s Mujahedeen, an Iranian group designated by the State Department as terrorists, who have been in American custody since 2003.

The new report, which has not received press attention, challenges the case made by some proponents of negotiations that fundamentalist Shiite Iran sees the fundamentalist Sunni Al Qaeda as a threat and would not cooperate with it.

“Whatever his whereabouts, Saif did not cease his Al Qaeda activities during this period,” the report says of Mr. Adel’s time in Iran.

As for whether Mr. Adel is in Iran today, the report is agnostic. “It is unclear whether Saif remains in Iran to this day, and if he is there, what his level of freedom of movement might be,” it says.

Among recent advocates for talks with Iran is Secretary of State Rice, who over the weekend insisted that all members of the Bush administration were supportive of reaching out to Iran, including Vice President Cheney. Last month, speaking from the deck of an aircraft carrier in the Persian Gulf, Mr. Cheney warned Iran against meddling in the Middle East.

Despite the assurances of Ms. Rice, Iran has escalated its rhetoric and actions against America.

Yesterday, Iranian officials denounced President Bush’s call for Iran to release three American citizens who were arrested last month on charges of espionage. The three Americans, who all have dual citizenship with Iran, were charged the day after Iran’s ambassador in Baghdad met for the first public bilateral talks with an American since the 1979 hostage crisis.

Over the weekend, more provocative statements came from Iran’s President Ahmadinejad, who told a gathering of diplomats in Tehran that the “countdown” to Israel’s destruction had started, a threat that carries even more gravity in light of Iran’s recent decision to install more centrifuge reactors in its uranium enrichment facility in Natanz.

The last confirmed correspondence from Mr. Adel occurred in 2005. In a memoir he wrote for an Arab journalist about Abu Musab al-Zarqawi, the late leader of Al Qaeda in Iraq, Mr. Adel wrote that he had not “met Abu Musab since he left Iran,” which was in 2002. The authors of the report say this implies that he was in Iran at the time of that writing.

But later on, the authors drop a tantalizing hint. A February 3 article from a London-based Arabic newspaper, Asharq al-Awsat, quotes the sister-in-law of a close confidant of Mr. Adel suggesting that Al Qaeda’s no. 3 man remains under house arrest from Iran’s Revolutionary Guard.

An American intelligence analyst asked about Mr. Adel’s whereabouts said the suggestion tracks closely with classified sources used in the new West Point report. “We keep close watch on this guy,” this source said. “If he was to leave Iran, we would know about it.”