Sir Hilary Synnott: Diplomat whose expertise was called on in the aftermath of the invasion of Iraq

Sir Hilary Synnott, who has died after a short illness, was regarded as one of Britain's greatest public servants and the most experienced of his generation in the affairs of his passion, the Indian subcontinent. It was entirely in character that he stepped into the breach when the Blair government needed a man to get it out of a mess in another part of the world – Iraq – after the 2003 invasion. The plea was made to him 10 days short of his retirement.

He had been home for only a few weeks after finishing three years as British High Commissioner to Pakistan, but acknowledged he would have "kicked himself" if he had not taken up the challenge. With Tony Blair's assurance that he could telephone him personally at No 10 if he needed anything, he took up a single suitcase, flew overnight to Kuwait, crossed the desert through a sandstorm into Iraq, and found that the "bloody mess" he had been warned about by a colleague was still worse than he had feared. For his first few days he lived without sheets, soap, or any means of communication. It was his first lesson in how completely the British in Iraq had to rely on the Americans. His reports to London all went by Yahoo and Hotmail via Washington.

The legacy of the six months he spent in Basra from July 2003 until January 2004 as southern regional co-ordinator of the Coalition Provisional Authority was to haunt him for the rest of his life. In January this year, three months before his final illness began, he felt stung to write to the Secretary of the Iraq Inquiry correcting statements made by Tony Blair on 14 and 21 January.

Sir Hilary had left Basra still hoping his engineering projects, provision of police and other measures to help civilians in Iraq's four southern provinces would be kept even after the sudden American decision to recall the United States's forceful chief in Baghdad, Paul Bremer, and wind up the CPA.

On that trust, of continuing multinational development presence in the south, he told Blair in his Valedictory Dispatch that "the balance of probability is positive."

But in response to Blair's evidence asserting that Sir Hilary had been "on balance optimistic not pessimistic" he wrote, on 24 January: "Had I known that the civilian capital, experience and impetus built up over the previous year would be allowed to fall away, thereby increasing the burden on the armed forces, I would no doubt have offered a different judgement." In his book Bad Days in Basra (2008), and in evidence to the Iraq Inquiry, Sir Hilary says he was given political support from London in principle, but this was not followed up in practice.

Tony Blair's rejection of his strategy in southern Iraq was not the only time the Labour government ignored Sir Hilary's advice. It was asked for and given before David Miliband's visit to India as Foreign Secretary in January 2009 but disregarded, and Miliband offended Indians by linking terror attacks such as those in Mumbai to the long-running dispute over Kashmir.

Almost up to his death Sir Hilary was giving advice on the renewed tensions between the United States and Pakistan. Asked for comments on the implications of the killing in May of Osama bin Laden, he laboured valiantly to type his thoughts on his Blackberry from his hospital bed.

He was expecting later this year to travel to Muscat, Delhi and Islamabad, and had been a consulting senior fellow from 2004 with the International Institute for Strategic Studies in London. Little supposing he had less than a year to live, the Commons Foreign Affairs Committee last October called him to give evidence about Pakistan and resolving the situation in Afghanistan, a question of personal interest in as well as professional, since he had two nephews in the Army. His conclusion was: "There is no silver bullet." In his final two years he helped the Army by giving talks on Afghan local customs.

Sir Hilary, whose time as High Commissioner in Pakistan coincided with the 9/11 attacks, had seemed in recent months to be to some extent disillusioned with the Pakistan military, suggesting it had to look inward.

Earlier, in his book Transforming Pakistan: Ways out of Instability (2009), he wrote: "Pakistan has paid a heavy price for other countries' behaviour towards it, notably the West's accommodation with the country's military rulers in the 1980s, and its encouragement of a jihad in the service of Cold War strategic goals."

Sir Hilary, a Hindi speaker, was unusual in having had a posting in India as well as Pakistan. He was Deputy High Commissioner in New Delhi between 1993 and 1996. On his death tributes came from leaders in both countries, calling him a good friend. He was previously head of chancery in Amman, Jordan, and head of security co-ordination in London in 1991 when the British hostages in Lebanon, Terry Waite, John McCarthy and Jackie Mann were released.

Hilary Nicholas Hugh Synnott was born in 1945 at Burnham-on-Sea, Somerset, son of a naval commander. He attended Beaumont College near Windsor and was a scholar at Britannia Royal Naval College, Dartmouth, before studying sciences at Peterhouse, Cambridge and the Royal Navy Engineering College and spending five years as a submariner. He then joined the Diplomatic Service, early posts including Paris and Bonn. He was made CMG in 1997 and KCMG in 2002. Peterhouse elected him to an honorary fellowship in January.

Hilary Nicholas Hugh Synnott, diplomat: born Burnham-on-Sea, Somerset 20 March 1945; CMG 1997, KCMG 2002; married 1973 Anne Clarke (one son deceased); died Southampton 8 September 2011.