Former Iranian president Mahmoud Ahmadinejad (centre) is surrounded by his supporters during the funeral ceremony of Iran's Ambassador to Lebanon Ghazanfar Roknabadi, who was killed in Saudi Arabia in a stampede at the Haj pilgrimage, in Tehran on Friday.

AFP/Tehran

Iran expects medical tests to establish within 48 hours if a high-ranking diplomat died on pilgrimage in the stampede at the Haj in Saudi Arabia, following contrasting accounts about his demise.

Ghazanfar Roknabadi, 49, a former ambassador to Lebanon, was initially reported as being among 464 Iranian pilgrims killed in the Haj’s worst-ever tragedy in September.

At least 2,236 worshippers perished in the giant crush at Mina, near the holy city of Makkah in western Saudi Arabia.

But suspicion has surrounded the circumstances of Roknabadi's death, with senior officials suggesting as late as two weeks ago that he was alive and being held hostage.

Iran finally confirmed on Thursday that Roknabadi's corpse had been identified in Saudi Arabia.

His body arrived back in Tehran on Friday with his coffin draped in the Iranian flag for a funeral ceremony.

Confusion over his death added to already heavy strain between Tehran and Riyadh, who back opposing sides in conflicts in Syria and Yemen.

Roknabadi was Tehran's envoy to Beirut, a highly sensitive post, until last year.

Lebanon is home to the Iranian-backed Shia movement Hezbollah, allied with President Bashar al-Assad in the Syrian civil war, who Riyadh has repeatedly urged to stand down.

Roknabadi's body was identified by DNA in Saudi Arabia but secondary testing will be used to determine if he died in the stampede, the ISNA news agency quoted his brother as saying.

"If the result of examinations in Tehran contradicts the Saudis' claim that my brother died in the Mina incident we will complain via international forums," Morteza Roknabadi said.

Giving a 48-hour timeframe for test results, he acknowledged the rumours about his brother's death, which included recent remarks by Iran's Deputy Foreign Minister Hossein Amir Abdollahian.

"Our intelligence indicates that he is still alive, and we ask Saudi Arabia to return him alive," Abdollahian said on November 11.

When Roknabadi was initially reported as being among the Haj victims, Iran's foreign ministry denied claims by some Arab media that he had travelled to Saudi Arabia under a false name.

On Friday, ministry spokesman Hossein Jaberi Ansari confirmed further testing would take place to establish how the diplomat died.

Top Iranian officials including supreme leader Ayatollah Ali Khamenei accused Saudi Arabia of incompetence at this year's Haj and said the handling of the aftermath and repatriation of bodies was far too slow.

However state media reported on Friday that Iran's Foreign Minister Mohammad Javad Zarif held a bilateral meeting with his Saudi counterpart Adel al-Jubeir on November 14 in Vienna.

The meeting, on the sidelines of international peace talks over Syria, is thought to be the highest direct engagement between Iran and Saudi since King Salman came to power in January.

ISNA and other news agencies said the ministers discussed the Mina stampede, the pilgrims still missing and legal aspects of the incident.