Seven years after the American activist Rachel Corrie was killed by an Israeli army bulldozer in Gaza, evidence has emerged which appears to implicate Israel's Gaza commander at the time, in an attempt to obstruct the official investigation into her death.

The alleged intervention of Major-General Doron Almog, then head of Israel's southern command, is documented in testimony taken by Israeli military police a day after Ms Corrie was killed on March 16, 2003. The hand written affidavit, seen by The Independent, was submitted as evidence during a civil law suit being pursued by the Corrie family against the state of Israel.

Ms Corrie, who was 23 when she died, was critically wounded when a bulldozer buried her with sandy soil near the border between Gaza and Egypt. The American, wearing a fluorescent orange jacket and carrying a megaphone, was among a group of volunteers from the anti-occupation International Solidarity Movement who over a period of three hours on that day had sought to block the demolition by Israel of Palestinian homes.

The Israeli military has maintained that its troops were not to blame for the killing of Ms Corrie and that the driver of the bulldozer had not seen her. It accused Ms Corrie and the ISM of behaviour that was "illegal, irresponsible and dangerous". Three days after Ms Corrie's death, the US state department announced that the Israeli Prime Minister Ariel Sharon had promised the US President George Bush that the Israeli government would undertake a "thorough, credible and transparent investigation".

But according to a military police investigator's report which has now emerged, the "commander" of the D-9 bulldozer was giving testimony when an army colonel dispatched by Major-General Almog interrupted proceedings and cut short his evidence. The military police investigator wrote: "At 18:12 reserve Colonel Baruch Kirhatu entered the room and informed the witness that he should not convey anything and should not write anything and this at the order of the general of southern command."

The commander was a reservist named Edward Valermov. He was in the bulldozer with its driver. In his testimony before he was ordered to stop, he told military police investigators that he had not seen Ms Corrie before she was wounded. Alice Coy, a former ISM volunteer activist who was near Ms Corrie during the incident said in an affidavit to the court that "to the best of my knowledge the bulldozer driver could see Rachel while pushing earth over her body."

Hussein Abu Hussein, a lawyer for the Corrie family, said Major-General Almog's alleged intervention blocked the possible emergence of evidence that could have determined whether Mr Valermov's assertion that he did not see Ms Corrie was reasonable. "Do I believe him? Of course not. There is no doubt this was manslaughter," Mr Abu Hussein said. "First of all we claim the state is responsible for the death of Rachel. And secondly we claim that the investigation was not professional."

"When you, the state of Israel, fail as an authority to perform your function of having a credible investigation, when your standard falls from reasonable, objective standards than you have caused evidentiary damage," Mr Abu Hussein said.

Contacted by The Independent, Major-General Almog, a hero in Israel for his role in the 1976 raid to rescue hostages in Entebbe, Uganda, denied ordering the bulldozer commander to desist from testifying. In 2005, the General narrowly escaped arrest in Britain on a war crimes charge for allegedly ordering the destruction in 2002 of 50 civilian homes in Rafah, where Ms Corrie was later killed. Major-General Almog was tipped off about the warrant and did not disembark at Heathrow, returning instead to Israel on the El Al flight.

Mr Valermov said in his testimony that the bulldozers, manned by two people, were ordered to continue their work despite the presence of the ISM protesters. He said that troops in an armoured personnel carrier threw stun grenades, used tear gas and fired shots towards the ground to scare the protesters away. "It didn't help and therefore we decided to continue the work with all possible delicateness on the orders of the company commander" he said.

The testimony was interrupted after Mr Valermov said the driver of the bulldozer, named only as Yevgeny, said he did not know if Ms Corrie had been harmed by the shovel of the D-9. "It was only when we moved the D-9 backwards that I saw her. The woman was lying in a place where the instrument had not reached. As soon as we saw the harmed woman we returned to the central corridor, stood and waited for orders." The soldier's last statement before the order to stop speaking was: "My job was to guide. The driver cannot guide himself because his field of vision is not large."

Another army document strongly suggests that Major-General Almog opposed the military police investigation. Dated 18 March 2003, a military police investigator petitioning a judge for permission to conduct an autopsy on Ms Corrie's body said that "we arrived only today because there was an argument between the general of southern command and the military advocate general about whether to open an investigation and under what circumstances." The judge granted the request provided the autopsy would be done in the presence of a US diplomat as the Corrie family requested. But the inquest was carried out by Israel's chief pathologist without any US official being there, in apparent violation of the judge's ruling.

Major-General Almog denied halting Mr Valermov's testimony. "I never gave such an order, I don't know such a document. I conducted my own investigation, I don't remember what I found. There were 12,000 terrorist incidents when I was general in charge of southern command. I finished seven years ago, if they want to invite me [to testify] they know the address. I certainly didn't disrupt an investigation, this is nonsense. In all of my service I never told anyone not to testify."

Asked if he gave an order to harm foreign activists interfering with the army's work, Major-General Almog responded: "What are you talking about? You don't know what a general in charge of command is. The general in charge of command has 100,000 soldiers. What are you talking about?''

Moshe Negbi, legal commentator for the state-run Voice of Israel radio, said of Major-General Almog's interdiction: "If a commander prevents a witness from testifying then it is disruption of an investigation, a criminal offence whose penalty is three years imprisonment."

Craig Corrie, Rachel Corrie's father, said the alleged intervention in Valermov's testimony was "outrageous."

"When you see someone in that position taking those steps you not only have to be outraged, you have to ask why is he covering up, what has he done that he needs to take these steps to cover it up?"

An Israel Defense Forces spokesman said: "Any military police investigations are completely independent and cannot be influenced by outside sources." The Israeli state attorneys handling the case declined to be interviewed. The trial is due to resume in September.

Rachel's nightmare scenario

Before she became a political symbol, Rachel Corrie was an American student on a study-abroad programme. A member of a middle-class family from Olympia, Washington, she was attending college locally when she travelled to Gaza with the intention of initiating a twin-city project between Olympia and Rafah.

Arriving in Gaza in January 2003, she linked up with the International Solidarity Movement, and spent the next two months as an activist. In the weeks before her death she wrote a series of emails home to her friends and family that detailed her impressions of life in Gaza. "I have bad nightmares about tanks and bulldozers," she told her mother. "I'm witnessing this chronic, insidious genocide and I'm really scared... This has to stop. I think it is a good idea for us all to drop everything and devote our lives to making this stop."

The emails, which later inspired a play that appeared in London but was cancelled in New York and Toronto, end with an exchange with her father. "I am afraid for you, and I think I have reason to be," he wrote. "But I'm also proud of you – very proud... But I'd just as soon be proud of somebody else's daughter."

Corrie died on 16 March 2003. Like the death of the British activist Tom Hurndall in similar circumstances a year later, it prompted an international outcry about Israel's deeds in the Palestinian territories.