Paris (AFP) - Iran has for years faced accusations of cooperation with Al-Qaeda despite stark ideological differences, but while mutual interests may have sometimes converged any relationship has been marked by distrust, analysts say.

US Secretary of State Mike Pompeo's claim -- made just a week before President Donald Trump leaves office -- that Iran was the "new Afghanistan" for Qaeda militants surprised observers, who said there was no evidence of the country being used as a base.

He also stated publicly for the first time that Al-Qaeda's number two, Abdullah Ahmed Abdullah, known as Abu Muhammad al-Masri, was assassinated in Tehran in August, buttressing allegations that Iran has at times offered sanctuary to the extremists.

On paper, Iran and Al-Qaeda are ideological foes -- the former the Persian regional heavyweight guided by Shia Islam, the latter inspired by a militant vision of Sunni Islam and dominated by Arabs.

Tehran has long dismissed claims of links to Al-Qaeda, and Iranian Foreign Minister Javad Zarif accused Pompeo of "ending his disastrous career with more warmongering lies."

Zarif noted that all the militants who carried out Al-Qaeda's 9/11 attacks on the United states came from Pompeo's "favourite ME destinations," a pointed reference to Iran's regional rival Saudi Arabia.

'Mutually suspicious'

Daniel L. Byman, a professor at Georgetown University, described the relationship between Iran and Al-Qaeda as "troubled and mutually suspicious." 

"In general, there is cooperation, and Iran does provide some sanctuary," he said, adding that "Iran has put limits on Al-Qaeda even as it has provided a haven".

The New York Times reported that Pompeo succeeded in "bewildering counterterrorism officials" with his comments, with some saying his assertions "appeared to represent his own analytic conclusions" rather than those of US intelligence.

"The relationship between Al-Qaeda and Iran since 9/11 has vacillated between periods of hostility and cautious accommodation," said Bryce Loidolt, a research fellow at the Washington-based Institute for National Strategic Studies.

Pompeo's comments came amid speculation that the Trump administration, in its final days, might go as far as ordering a strike against Iran -- even as incoming president Joe Biden mulls rejoining the 2015 deal on its nuclear programme.

Some analysts, citing intelligence data including the documents found in Osama bin Laden's final hiding place in Pakistan, argue that contacts have existed between Al-Qaeda and Iran for decades.

But the most significant Iranian help was to offer sanctuary for militant leaders just across the border from Afghanistan, and the closeness of ties has depended on the political climate.

The killing of Abdullah in Tehran, reportedly carried out by Israel's Mossad agents at the behest of the United States -- though this was not confirmed by Pompeo -- has also thrown new light on the alleged presence of Qaeda members in Iran.

After 9/11 many Al-Qaeda cadres from Afghanistan did seek refuge in Iran but it was never an easy relationship, Loidolt said, leading up to a wave of arrests in 2002 and 2003.

"Iranian willingness to tolerate the presence of Al-Qaeda members did not come without conditions," Loidolt wrote in an article for the Studies in Conflict and Terrorism journal. 

'Way too valuable'

Assaf Moghadam, associate professor at the Interdisciplinary Center Herzliya (IDC) in Israel, described the relationship as "tactical cooperation."

"Offering a safe haven to Al-Qaeda members in Iran does not only give Iranians a potential option to threaten the United States, but it has also worked as an insurance against Al-Qaeda attacks directed in Iran," he said.

Especially with the US administration changing, he said, Iran will not want to give up an "Al-Qaeda card" that has proved "way too valuable" for Iranian leaders in the past.

Moghadam has himself argued that relations have existed between Iran and Ayman Al-Zawahiri, Al-Qaeda's top idealogue and Bin Laden's successor, since the 1990s.

In 2015, a US court found Iran liable over the 2000 Al-Qaeda bombing of the USS Cole warship in Yemen, saying Tehran had helped build its network in the country and supported training in the region.

But beyond these episodes of cooperation, the relationship has remained one of hostility and distrust.

"This is held together not by trust but by mutual threat and the ability of each side to harm the other if they break out of the agreed guidelines of the relationship," said Barak Mendelsohn, an associate professor at Haverford College in Pennsylvania.

Byman said Iran could even be prepared to hand over Al-Qaeda operatives to the US to face justice if tensions eased, but said this was clearly unlikely given the current tensions between the two countries.

Depending on the political climate, Iran "would be happy to sell out Al-Qaeda, but only for the right price," Byman said.