"Iran has repeatedly resisted numerous calls to transfer custody of its AQ detainees to their countries of origin or third countries for interrogations or trial," the report says. "Iran also continued to fail to control the activities of some AQ members who fled to Iran following the fall of the Taliban regime in Afghanistan."
But U.S. officials tell ABC News that one reason they have not raised the issue more publicly is that they believe Iran has largely kept these al Qaeda operatives under control since 2003, limiting their ability to travel and communicate.
"It's been a status quo that leaves these people, some of whom are quite important, essentially on ice," said a U.S. official.
Iran has its own reasons to keep these militants under house arrest. Al Qaeda is a Sunni Muslim group that has a complicated, sometimes tense, relationship with Iran. Recent public statements by al Qaeda have taken an unusually anti-Iranian tone. In two audiotapes released last month, for example, Zawahiri lambastes the Iranian government for, among other things, trying to take over southern Iraq.
So, why would Iran now be reaching out to al Qaeda? U.S. intelligence analysts have several theories. Under one theory, the talks are a reaction to al Qaeda's recent anti-Iranian rhetoric. The Iranians are using the al Qaeda detainees as, the theory goes, leverage — "hostages" in the words of one official — to get al Qaeda to cut its recent anti-Iranian rhetoric and to deter any potential al Qaeda operations against Iran. By detaining them, Iran makes an unspoken threat to al Qaeda's leadership: If al Qaeda attempts to attack Iran, these people will suffer.
Others believe Iran may have initiated the talks as a threat to the United States, that if the U.S. takes hostile action against Iran, these captives could be released, set free to plot attacks against the West.
One senior U.S. official says there are ongoing "tensions and flirtations" between al Qaeda and Iran "with al Qaeda very much interested in trying to get these guys released and back in the fold, and with Iran playing strategic games knowing that al Qaeda is ultimately their enemy."
Adding to the concern about this, the intelligence community has only limited knowledge about the status of the al Qaeda operatives in Iran and even less about what Iran intends to do with them. Asked if the U.S. knows where Iran is holding them, a high-ranking U.S. military officer told ABC News, "No. I wish we did."
ABC News interviewed several high-level U.S. national security officials for this story. Because of the sensitive nature of intelligence on this subject, all spoke on the condition that their names not be used. We also asked the government of Iran to comment on this story. The spokesman for the Iranian Mission to the United States said he could not answer our specific questions but told us combating terrorism "remains one of the main Iranian political priorities."