As archbishop of York, John Habgood, who has died aged 91, pushed through a compromise position on the ordination of women in 1992 that many in the Church of England felt to be a betrayal.

Although he was intellectually and theologically in favour of women priests – telling the General Synod to remember that God was neither male nor female – he nonetheless led the bench of bishops and the General Synod to support his idea that “two integrities” should be allowed within the church: one that could accept women priests and another that could not. It was an awkward squaring of the circle that left women to pay the price.

Over the years Habgood had consistently voted in favour of female priests, but in the final analysis it felt as if his heart was not with his mind. At the crucial General Synod decision on the matter he voted again in favour, but then immediately took action to appoint a group of provincial episcopal visitors – the famous “flying bishops” – who were assigned to minister to those who refused to accept the ordination of female priests.

In doing so he miscalculated the reaction of parliament, which was to accept women priests enthusiastically: with majorities of 105 in the House of Lords and 194 in the House of Commons. So it was that Habgood, a consistent ecumenist, persuaded the church to accept a profound institutionalised division, even if in the cause of preserving unity.

Before serving at York (1983-95), a post second only to the archbishop of Canterbury in the church hierarchy, Habgood was bishop of Durham for a decade. He described himself as a conservative-liberal: conservative because of his establishment background, and liberal because he claimed to see six sides to most religious questions. Widely respected inside and outside the Anglican church, he provided a reasoned voice in ethical debates in the Lords as well as in the thinking of the church’s Board for Social Responsibility. Like Robert Runcie, with whom he worked closely, he believed in consensus both in church and state.

Facebook Twitter Pinterest John Habgood, right, during the Queen’s visit to York Minster in 1988 to unveil a plaque commemorating the restoration of the south transept and the famous Rose Window. Photograph: Neil Munns/PA

Though he was a tall, shy, smiling figure, his manner could sometimes be distant, as he demonstrated in 1988 when hosting 1,400 women who were offering themselves to the ministry of the church. Many had travelled hundreds of miles at their own expense, but arriving at York Minster for a eucharist were fed up to find a shortage of chairs, bread and wine for the communion and to receive a sermon from Habgood that sounded as if it came from a headteacher unhappy at the possible influx of rowdy pupils.

He did not do justice to their dedication and commitment and this tendency to remoteness was a factor in prompting some clergy and laity to campaign against any moves to make him bishop of London in the early 1980s and then archbishop of Canterbury in the early 90s.

Born in Stony Stratford, Buckinghamshire, John was the son of Arthur Habgood, a GP, and his wife, Vera (nee Chetwynd-Stapylton). After attending Eton during the second world war he went to King’s College, Cambridge, where he gained a double first in natural sciences. He was taken on by the Medical Research Council in lieu of national service and in 1950 became a demonstrator in pharmacology at Cambridge, helping students with their work while carrying out research for a PhD in the physiology of pain (1952).

Habgood had paid little attention to religion until he joined the Christian Union at Cambridge in 1947, but by 1953 he had decided to enter the Church of England, beginning 18 months of training at Cuddesdon Theological College in Oxford. Still donnish, he was first ordained to a curacy at St Mary Abbots in Kensington, London, in 1954, and two years later returned to Cambridge to teach theology as vice-principal of Westcott House, remaining in that position until 1962.

At that point, having married Rosalie Boston, a musician and music teacher, in 1961, he became rector of St John’s Church, Jedburgh, in the Scottish Borders, where three of his four children were born. In 1967 he moved to become principal of Queen’s College, Birmingham (now The Queen’s Foundation), which, after a merger with Handsworth Methodist College in 1970, became the first ecumenical theological college in the UK.

He was at his best there, enabling Anglicans, Methodists and others to train together for the ministry. But he was called upon to succeed Ian Ramsey as bishop of Durham in 1973, simultaneously becoming a member of the Lords.

Habgood personified the tradition of academic bishops in Durham and York, and promoted fresh thinking on the ethical problems posed by scientific development. He wrote a number of books on his chosen themes, including Science and Religion (1964), A Working Faith (1980), and Church and Nation in a Secular Age (1983). His thoughts on ethical questions in science and religion provided guidelines for the thinking believer at a time of new behavioural patterns in sexual ethics and discoveries in genetics and bioproblems.

On retirement in 1995 he was made a life peer, sitting as a crossbencher, and for three years chaired a government committee on xenotransplantation (from one species to another). In 2011 he retired from the Lords.

Rosalie died in 2016. He is survived by their children, Laura, Francis, Ruth and Adrian.

• John Stapylton Habgood, Lord Habgood, prelate, born 23 June 1927; died 6 March 2019

• Alan Webster died in 2007

• This article was amended on 9 March 2019. The phrase “Anglicans of all kinds – Methodists and others” was rewritten as “Anglicans, Methodists and others”.