Air crash experts have raised serious concerns over the handling of the crash site of a Ukrainian airliner suspected to have been accidentally shot down by Iranian missiles, as fears grow that Tehran has sought to eliminate evidence from the area.

Graham Braithwaite, professor of safety and accident investigation at Cranfield University, said the Iranian handling of the crash site, including the apparent quick removal of evidence, raised “serious concerns over the integrity of the investigation”.

“Where you have flight recorders that tell you what has happened you can move quickly to clearing the site,” he explained. “But if the recorders are damaged [as the Iranians have said] then all you have is the forensic evidence at the site to tell you the story.”

The Ukrainian foreign minister, Vadym Prystaiko, said on Friday that it had been given access to the flight recorders and planned to start analysing their content.

Iran has invited investigators from Canada, Ukraine and Boeing to see the accident site on the outskirts of Tehran to prove the aircraft was not mistakenly targeted by Iranian air defences. It said it would also welcome representatives of other countries whose citizens died on Ukraine International Airlines flight 752.

Prystaiko said Ukrainian experts had been given access to the crash site but according to a crew from the US broadcaster CBS News who reached the crash site by 9am on Thursday morning, it appeared to have been cleared of the plane’s debris. “Scavengers now picking the site clean,” said Elizabeth Palmer, a CBS correspondent. “No security. Not cordoned off. No sign of any investigators.”

Elizabeth Palmer (@elizapalmer) CBS crew just visited the #Ukrainian airlines crash site west of Tehran. Nine am local time. Virtually all pieces of the plane were removed yesterday - say locals. Scavengers now picking site clean. No security. Not cordoned off. No sign of any investigators. pic.twitter.com/hhNJyokhjq

Braithwaite, who teaches a course in air accident investigations, said he was surprised that the Iranians had moved to clear the crash site before other interested parties, including Ukrainian, Canadian and other technical investigators had been able to make their own examination, which he said he would have expected under annexe 13 of the Chicago convention, the international agreement that sets out protocols for crash inquiries.

Braithwaite said he was also surprised to see images of an earthmover moving debris at the crash site – suggesting that risked compromising the scene – as well as the CBS report that the site had been left unsecured while local residents scavenged.

“It suggests poor site discipline at least, or wilful neglect. If a site is picked clean you can’t put it back together again.”

He said accident investigators were usually mindful of doing anything that might compromise a criminal investigation, particularly relating to the chain of custody of evidence that might contain explosive residues. “You would expect the protocols involved then to be of the highest standards overseen by police or security forces.”

The plane with 176 passengers and crew onboard went down shortly after taking off around 6.13am on Wednesday morning, about five hours after Iran had launched a volley of missiles at US forces stationed in Iraq, and while it was on high alert for possible retaliation.

Play Video 2:15 What we know about the Iran plane crash that killed 176 people – video report

Iran’s semi-official Fars news agency said the country will announce on Saturday the reason for the crash, citing an informed source. Western intelligence sources told the Guardian on Thursday evening they believed the aircraft might have been shot down by two surface-to-air missiles in what one source described as “a tragic accident” but Iran has so far rejected that possibility.

Photographs taken the day of the crash showed heavy machinery being used to move larger pieces of debris. Iranian media also published several photographs and videos of the wide field of wreckage and personal belongings left by the crash.

It was unclear whether the removal of the debris was done in accordance with crash investigations procedures to ensure important evidence is preserved.

The veteran British aviation analyst David Learmount, who has written extensively on flight safety issues, also expressed his shock over the conduct of the Iranian investigation.

“The Iranians are signatories to the Chicago convention and they know what the protocols are,” he said. “You don’t work as fast as this to clear the site. It really is too bloody fast. You don’t do it in 24 hours. One thing is all accidents like this should be treated as a crime scene.”

Learmount said he would have expected other interested parties to the crash to be allowed to examine the scene before debris was removed. “The Iranians know all this. They know what they should be doing. They are entitled to be in charge of the investigation but even then they don’t have to carry it out themselves. They can get help from outside.”

On Friday, Iranian officials continued to deny that the aircraft was shot down. Ali Abedzadeh, the head of Iran’s Civil Aviation Organisation, said at a press conference in Tehran: “If [intelligence agencies] have findings with scientific support they should show this to the world.”

He said he had watched a video clip purporting to show the plane being hit by a missile before crashing to the ground but said “this cannot be confirmed from the scientific perspective”.

Speaking in London, Iran’s ambassador to the UK, Hamid Baeidinejad, said it was untrue that the crash site had been bulldozed and said the bodies had been removed but that relevant debris was being retained along with the black boxes. He did not specify if the wreckage was being kept at the crash site or taken elsewhere.

“[I am] disappointed that some countries including the UK, which do not have hard evidence, without access to the black box, the voice recordings, airplane wreckage and the technical engineers reports in Tehran airport, are rushing to judgment,” he said. “That only adds to the anxiety of the families.”

Hassan Rezaeifar, the head of the committee that oversees aviation accidents in Iran, said that, contrary to earlier claims that the black boxes appeared to have been damaged by the crash, both appeared to be intact.

“We prefer to extract the data and download the data inside the country,” he said. “But if we come to the conclusion that the data may be damaged then we will carry out the process [overseas].”

Investigators would attempt to extract and analyse the black box data on Friday, he added, but the findings might take one or two months to be released.

The German foreign minister, Heiko Maas, encouraged Iran to be transparent. “It is important now that this is fully explained,” he said. “This cannot be hidden under the table. If that were to happen then it would breed new mistrust and that is the last thing we need now.”