The strategy included internment of leaders and activists, closure of radio stations and replacement of imams in mosques – the bulk of which has since been carried out.

Two documents drafted by the Secret Intelligence Service in conjunction with other Whitehall departments, which are among the cache given to al-Jazeera TV and shared with the Guardian, are understood to have been passed to Jibril Rajoub, former head of PA security in the West Bank, at the beginning of 2004 by an MI6 officer then based at the British consulate in Jerusalem.

The evidence uncovered by the leaked documents highlights the role British officials and security advisers have played in creating and bolstering the PA administration in the West Bank, which is backed and financed by the US, the EU and most Arab states as it pursues what are now all but moribund peace talks with Israel.

Hamas, which won the Palestinian elections in 2006 and is backed by Iran and Syria, carried out dozens of suicide bombings in Israel from the mid-1990s and was the target of Israel's attack on Gaza in late 2008. It opposes negotiations with Israel except on a long-term ceasefire and will not recognise it. Palestinian Islamic Jihad, a smaller group, has similar positions.

The PA is increasingly the target of domestic and international criticism for authoritarian rule and human rights abuses, including detention without trial and torture.

The British papers, one of which is headed Palestinian Security Plan – Confidential, included detailed proposals for a new security taskforce based on the UK's "trusted PA contacts" outside the control of "traditional security chiefs", a British/US security "verification team", and "direct lines" to Israeli intelligence.

Issues include suicide bombing, weapons smuggling, Qassam rockets and "terror finance". The SIS and other leaked British official documents have been independently authenticated by the Guardian.

In the most controversial section, the 2004 MI6 plan recommends "Degrading the capabilities of the rejectionists – Hamas, PIJ [Palestinian Islamic Jihad] and the [Fatah-linked] Al Aqsa Brigades – through the disruption of their leaderships' communications and command and control capabilities; the detention of key middle-ranking officers; and the confiscation of their arsenals and financial resources".

The document adds: "We could also explore the temporary internment of leading Hamas and PIJ figures, making sure they are well-treated, with EU funding" – reflecting a concern to distance the intelligence agency from the PA security organisations' established reputation for prisoner abuse.

The MI6 strategy, which was drawn up to implement George Bush's Middle East "road map" as the second Palestinian intifada was winding down, can then be traced through a sequence of more public Palestinian, EU and British documents and plans, and has now been largely implemented by the US and British-advised PA security apparatus.

The leaked intelligence plan can be seen in retrospect as a blueprint for PA security control of the West Bank, which has become harsher and more extensive since the violent takeover of Gaza by Hamas in the summer of 2007. Hundreds of Hamas and other activists have been routinely detained without trial at a time in recent years and subjected to widely documented human rights abuses.

In a meeting with US official David Hale in September 2009, the PLO chief negotiator Saeb Erekat is recorded as saying that PA prime minister Salam Fayyad was "doing everything possible to build the institutions. We are not a country yet but we are the only ones in the Arab world who control the Zakat [charitable religious donations] and the sermons in the mosques" – echoing what had been proposed nearly six years earlier by British intelligence.

The former MI6 officer Alistair Crooke, who worked for the EU in Israel and the Palestinian territories, said today that the documents reflected a 2003 decision by Tony Blair to tie UK and EU security policy in the West Bank and Gaza to a US-led "counter-insurgency surge" against Hamas – which backfired when the Islamists won the 2006 elections.

The CIA played the central role in building up PA security forces from the late 1990s, in close co-operation with the Israeli military and intelligence, detailed in the leaked documents. But particularly after the killing of three US officials in the Gaza strip in 2003, British forces played an increasingly active role – though always in close co-operation with their counterpart US agency, according to diplomatic sources.

The sequence of leaked British documents begins with an unmarked but detailed MI6 draft of the security plan, faxed from the Egyptian embassy, at a time when the agency was working closely with Egyptian intelligence; continues with the second more formal paper jointly drafted by SIS, which floats internment; and is then translated into a series of official papers drafted by the Jerusalem consulate's military liaison office, which liaises with British special forces, the SAS and SBS.

The documents confirm that by 2005, British projects under the Palestinian security plan – first drafted and passed to the PA under MI6 auspices – included extensive funding of the most controversial parts of the PA security apparatus, including general intelligence, special forces and preventive security under the heading of "UK-Palestinian projects".

The last in particular has been the subject of repeated and widespread allegations and evidence of torture, including by Amnesty International and Human Rights Watch. More recently, the British government has denied directly funding the PA's preventive security.

US general Keith Dayton, who, along with a string of British deputies was in charge of building up Palestinian security forces as US security co-ordinator for Israel and the Palestinian territories until last October, is recorded in the leaked Palestinian records as complaining about torture by PA intelligence in a meeting with chief PLO negotiator Saeb Erekat in June 2009. "The intelligence guys are good. The Israelis like them," Dayton says. "But they are causing some problems for international donors because they are torturing people", adding: "I've only started working on this very recently. I don't need to tell you who was working with them before" – in an apparent reference to the CIA.

In an interview with al-Jazeera, former Dayton deputy US colonel Phillip Dermer described the PA as constituting a "police state" and its security forces as an outsourced "third Israeli security arm".

Many of those now arrested and detained in the West Bank appear to have no connection to any armed group or activity. Records of a May 2008 meeting between Israeli general Amos Gilad and the head of PA security forces, Major General Hazem Atallah, refer to a senior Israel security official identified as "Poly" who asked: "How is your fight against 'civilian' Hamas: the offices, people in municipalities etc? This is a serious threat."

Atallah is recorded as replying: "I don't work at political level, but I agree we need to deal with this" – to which Poly retorts: "Hamas needs to be declared illegal by your president. So far it is only the militants that are illegal."

Another leaked PA security document from 2005, drawn up by a Palestinian official, confirms the central role played by British officials in "unifying Palestinian security efforts" and identifies a former PA senior security figure, Bashir Nafi, as having "strong ties with the British".

Along with Abed Alloun, Nafi was a deputy to Rajoub. Alloun and Nafi were killed in a bomb attack in Amman in 2005. Alloun, a Liverpool football fan, told the Guardian in 2003 he had been flown by MI6 to Britain and taken to see Liverpool play at Anfield and given a ball signed by Michael Owen.