Scotland Yard allowed a suspected war criminal to escape Britain because officers feared an attempt to stop him would lead to a gun battle at Heathrow airport, police documents seen by the Guardian reveal.

The former senior Israeli officer was supposed to be detained as he arrived in London for a speaking engagement after a British court had ordered his arrest.

But detectives watched on as he landed and hid on the plane for two hours, before flying off to escape justice.

In the documents, counter-terrorism police say they did not try to board the Israeli civilian jet partly because they feared armed guards on the plane would open fire on British officers.

A UK court had issued a secret arrest warrant for Major General Doron Almog over alleged war crimes under the Geneva conventions of ordering the demolition of 59 civilian Palestinian homes.

Israeli diplomats were tipped off after Almog's plane left Israel on September 11 2005. Once it landed in London, a military attaché from the Israeli embassy boarded the jet and warned Almog to stay on board. He refused to leave the plane until it took off again for Israel, two hours later.

UK police were waiting to arrest him at the immigration desk inside the terminal.

The war crimes arrest warrant was issued by senior district judge Timothy Workman, after an application by British lawyers acting for Palestinian victims of the demolition in 2002, in Gaza.

Under British law, war crimes should be treated so seriously that even if they are committed abroad, UK courts have jurisdiction to try suspects.

Almog, commanding officer of the Israeli defence forces' southern command from December 2000 - July 2003, was due to arrive at Heathrow airport at 1.25pm on a flight belonging to El Al, Israel's national carrier. The airline refused Scotland Yard permission to board the plane.

Those who obtained the warrant say the police made errors.

The document is written by detective superintendent John MacBryane, from the counter-terrorism command, who was in charge on the day Almog arrived in London. It was drafted by Scotland Yard as part of their response of an investigation into the incident by the Independent Police Complaints Commission.

It forms a summary of the decision log, detailing what actions police took and why.

MacBrayne wrote of events the day Almog landed at Heathrow: "By 2.30pm it became apparent that Mr Almog had not presented himself at the Immigration desk. A check of the flight manifest revealed that Mr Almog was on the plane, possibly in company with his wife.

"Consideration was given to boarding the El Al flight and DSU MacBrayne sought clarification of his powers to do so with those officials present."

Top detectives were told that police routinely boarded flights, but were not sure if they could do so without the permission of the airline.

"It was confirmed that El Al were refusing voluntary access to the plane and DSU MacBrayne could not get confirmation that he had a legal right to do so. The time scale involved made it impossible to receive the appropriate advice before the El Al flight was due to return to Israel at 15.30 hrs …

"Another consideration being that El Al flights carried armed air marshals which raised issues round public safety. There was also no intelligence as to whether Mr Almog would have been traveling with personal security as befitted his status, armed or otherwise."

"DSU MacBrayne took the considered opinion that, as access to the plane would not be consensual, there existed a real threat of an armed confrontation."

Detectives considered boarding the plane with armed officers, but felt this "presented an exponential risk to the officers, especially with the lack of intelligence regarding personnel on the plane".

"In light of the above, the decision was made not to approach/board the aircraft."

Daniel Machover, a solicitor involved in gaining the warrant on behalf of Almog's alleged Palestinian victims, said police did not need permission to board the plane. He said they should have told the airline: "You're on British soil, we're coming aboad."

Machover said police could also have stopped the plane taking off until Almog emerged.

The document reveals that before the planned arrest, Scotland Yard consulted West Midlands police and a special police unit called the national Communities Tensions Team, for advice on reaction in the British Jewish community. A "trusted partner" of the police, a Jewish contact, also made inquiries about finding a lawyer for Almog and raising his bail money, once he was arrested. The document says the inquiries were made "discreetly" without Almog's name being mentioned.

But Machover said it would have been obvious that the inquiries were about Almog: "If you go about making inquiries of this kind, it is easy for someone to put two and two together and work out the inquiries are to do with Almog."

The arrest warrant was issued at Bow Street magistrates court, central London. It was believed to be the first warrant for war crimes of its kind issued in Britain against an Israeli national over conduct in the conflict with Palestinians.

The attorney general would have had to sanction the war crimes prosecution before it went ahead.

Speaking days after avoiding the arrest, Almog told the Guardian that as he prepared to leave the plane, he was advised to wait by the cabin crew. Israel's then military attaché in London arrived on the plane to inform him that he faced arrest.

The 55-year-old former general said: "I don't know how he [the military attaché] found out but I am glad he did. It was also fortunate that I was flying with El Al as they are loyal. I don't know what would have happened if I had been on a British Airways flight."

Almog said: "As a soldier and a general, I have never committed a crime. Many times I have saved Palestinian lives by risking my life and the lives of my soldiers."

The actions of the Israeli army in Gaza were to prevent terrorist attacks against Israel, he said.

Raji Sourani, the director of the Palestinian Centre for Human Rights, said: "Failure to respect the rule of law and to pursue those responsible for attacking civilians will undermine the respect for international law which we do badly need if we are to have peace in our region. Until such time we will be faced with the rule of the jungle."