As Conservative MP for Thirsk and Malton, Anne McIntosh proved herself experienced, hard-working and loyal. Yet last week she was deselected after a long and bitter wrangle – yet another setback for women in the Conservative party

For the Conservatives, trailing Labour by nine points among women voters in the latest polls, last Friday headline was a problem. Anne McIntosh, the MP for Thirsk and Malton in North Yorkshire and the only female Tory MP in Yorkshire, had been deselected by her local party following a bitter battle that, it emerged, stretched back years. There had even been an attempt to deselect her back in 2009, before she was even elected.

Her enemies were men. Their leader was local party chairman Major Peter Steveney, a former cavalry officer and Jockey Club official. Their ranks comprised a bunch of disgruntled local businessmen. Waiting in the wings to ride to their rescue was Edward Legard, another former army man, local councillor, barrister, baronet, defeated Conservative candidate for Darlington in the 2010 general election and a contemporary of the prime minister at Eton.

McIntosh, 59, is a senior politician and the only female Conservative to chair a select committee. She is scrupulously hardworking and loyal, attending more votes than most and rebelling extremely rarely. What's more, she is half-Scottish, born in Edinburgh, and, as chair of the environment committee, knows all about flood defences at a time when the government faces accusations of incompetence, and when environment secretary Owen Paterson has had to take time off for an operation.

After losing the ballot of her 560 local association members, which was only held because Conservative Central office overruled a decision to ditch her more than a year ago, McIntosh first suggested she would stand in Thirsk come what may, then went on television to accuse her detractors of "ungentlemanly behaviour". Coming just 10 days after another MP, Jessica Lee, announced she would stand down in 2015, the fourth Conservative woman from the 2010 intake to do so, here was clear proof of the party's problem with women and clubbishness. Wasn't it?

I sit down with McIntosh over a pot of tea in the House of Commons. How was the conduct of her local association "ungentlemanly"? Did they bully her? Gang up? What did she expect? Is chivalry the norm in this corner of North Yorkshire, where the Conservative association has the famous setting of Brideshead Revisited, Castle Howard, as the main image on its website?

But McIntosh, it turns out, has moved on. Having begun the interview by announcing that she wants to be profiled by the Guardian but does not want to talk about the most dramatic week of her political life, she launches into a list of her greatest achievements.

It seems a good idea to know something of the hinterland of this experienced female politician who seems to have found her local Conservative party such an awkward fit, so I listen as she runs through her CV.

"I went to Harrogate Ladies' College and was very good at history. I won the Bertha Smith prize for history, of which I'm very proud," she says.

Then came law at Edinburgh and a scholarship to Aarhus university in Denmark to study European politics (McIntosh's mother was Danish). From 1983 she worked in the European parliament; she joined the Conservative party in the mid-80s, and "never strayed from having Conservative views".

So how did it go so wrong for her in Yorkshire? Were there big rows?

"Any association is like a family and from time to time there will be disagreements," she says. She never meant that she would stand as an independent against the official Conservative candidate: "My statement was a bit misconstrued, I was disappointed."

Isn't she heartbroken at the prospect of losing the job she loves?

"You have to take the rough with the smooth. I've still got a job." Parliamentary colleagues, she says, "have wrapped a comforting arm around me this week".

What about the attack on her by Martin Vander Weyer, the business editor of the Spectator who happens to be a constituency association member, and witnessed the showdown at last year's AGM? In an article this week he defended Steveney and blamed McIntosh's venomous, paranoid personality for "setting neighbour against neighbour". The Daily Telegraph's Peter Oborne called his piece "one of the most important articles written about politics this year".

"Martin and I know each other extremely well, and Martin did apply for the seat I was eventually selected for in the Vale of York [where she was MP before Thirsk], but I would hope that we're friends and can rise above that kind of rivalry," is McIntosh's answer. In other words, she dismisses Vander Weyer's opinion as sour grapes.

McIntosh is one of only six MPs deselected in this way in the past 25 years. Isn't it a weird position to be in – being sacked but with 15 months' notice to work out until the general election?

"Yes, and I'm not running away. The chairman and I have known each other for years, and we'll work our way through the differences. I could have run away this week and hid my head between my legs, but I wanted to show people there are no hard feelings."

Remarkably, given all that has happened, McIntosh still believes she has a chance of being re-elected as the Conservative MP for Thirsk. "The official position, according to the rules, is that I remain a Conservative party candidate and can apply for any seat, including the seat I currently represent."

‘The prejudice Anne has faced is awful’ … Margot James, Conservative MP for Stourbridge. Photograph: Antonio Olmos for the Guardian

How to go about this is the question, and McIntosh is still working on her tactics (and her media strategy: having agreed to pass on the phone number of one of her supporters at the end of the interview, she ignores my emails). Clearly, if she is to have a hope, she has to win back some of the Yorkshire Conservatives who have deserted her. She insists she is looking forward to a face-to-face meeting in the next few days, says how magnanimous Steveney has been in victory, and delivers a short lecture about flood defences in Pickering.

But her best and probably her only hope of a comeback is an open primary, and she will need help from higher up if she is to persuade her local party that this is the way to run their selection. She believes she has better standing in the constituency, among Conservative voters, than with activists, and that in a bigger pool she could win the race. Will Central Office intervene? And with European and local elections coming up, does support from London help or harm her?

Commentators such as Oborne, who believe the Conservative leadership has become dangerously out of touch with traditional supporters, have already pounced on comments supportive of McIntosh made in the House of Commons by Andrew Lansley and Speaker John Bercow. In Oborne's view this is undemocratic meddling: an MP's relationship with their association is sacred and if it goes wrong, it's their problem.

Others have suggested support for McIntosh on the Conservative frontbench is not as strong as it might be, and compared the muted response to her deselection with the backing offered by ministers to Tim Yeo, deselected by his South Suffolk association just a few days later. This week she sat immediately behind David Cameron at Prime Minister's Questions on Wednesday, a placement intended to offer comfort that backfired spectacularly when it turned out there was not a single woman on the Conservative front bench.

McIntosh has been an MP since 1997, when she entered parliament as MP for the Vale of York as one of a group of five new Conservative women she calls the "famous five": herself, Theresa May, Julie Kirkbride, Caroline Spelman and Eleanor Laing. This was to be the new dawn for women in politics. Following Labour's use of all-women shortlists, in Tony Blair's first term there were 101 Labour women.

For the Conservatives, of course, this meant 13 years in opposition. While McIntosh had several frontbench positions, she never made the shadow cabinet. In 2010, the death of her Ukip opponent in Thirsk shortly before the election saw the local poll postponed. By the time McIntosh was elected three weeks later with a majority of 11,000 (on a turnout of 50%, the lowest in any Conservative seat in the country), the ministerial jobs had been handed out. As she told the Yorkshire Post last year, she was disappointed. So should we conclude that sexism is the reason women so often fail to get ahead in politics? Or the reason why, even when they do, they are sometimes forced to retreat after just a few years, bruised by the boys' club atmosphere or "chumocracy", penalised along with their families by the punishing hours and travel to and from London, targeted by "ungentlemanly" taunts in person and by the press?

None of the four Conservative women who have announced they are standing down after five years wanted to talk to the Guardian about their decisions. McIntosh thinks women are "in quite a good place in politics". She takes some of the blame herself: "I'm half-Danish, half-Scottish, my husband compares me to Saga [Noren, the detective widely seen as having Asperger's] in The Bridge. I will accept I'm very difficult to work with. I think Margaret Thatcher was difficult to work with, or a difficult person, but I think she got things done."

Other Conservative women readily admit there is a problem while pointing out that the situation for Liberal Democrats is far worse (the Lib Dems have no women in cabinet, and just seven women MPs). Margot James, Conservative MP for Stourbridge, says "the prejudice Anne has faced is a spectacularly awful example" of what can happen and that, though it doesn't bother her, "occasionally, especially at PMQs, you do feel you don't fit in". Another female Conservative MP, who asked not to be named, said of her departing colleagues: "They're being very loyal, but I think for women in Westminster [the problem is] the culture, and because it's such a blokey culture it works in a certain way." For example, on a recent away day, the two socials were a football match and a visit to a car factory.

Increasingly, and perhaps with an eye on polls that show Conservatives losing support from the very women voters who consistently favoured them until 2005, men are making similar complaints. Bernard Jenkin recently called for "zero tolerance" of the unconscious slights towards women that "we men are all guilty of", while Conservative Home's Andrew Gimson said women felt "excluded from the rooms where the meaningful discussions are taking place". Whether the Conservative party can boost the position of its remaining women MPs and persuade local associations to select lots more before next year, while simultaneously reinvigorating its base by granting the grassroots more power and increased autonomy, is doubtful. These are both modernising causes and they conflict. Expect plenty more argument about which should come first.