Pete Wishart quit the SNP front bench in the House of Commons and accused Mr Flynn of a rebellion to bring down former leader Ian Blackford.
Defence spokesman Stewart McDonald, one of the SNP’s most prominent MPs, also quit his role after Mr Flynn vowed to ‘shake things up’, while its chief whip was axed.
As tensions heightened in the party, Miss Sturgeon refused to repeat her previous assertion that there had not been a coup to bring down Mr Blackford.
Scottish Tory chairman Craig Hoy said: ‘The SNP are fighting like ferrets in a sack. Their longest-serving MP is clearly unhappy at Stephen Flynn’s boasts about wanting to “shake things up” and Nicola Sturgeon losing her once vice-like grip over the party.
‘Despite claiming he will give the new Westminster leader his full support, Pete Wishart’s damning letter is the latest evidence of the deep splits running through the SNP.
‘His scathing attack on Stephen Flynn for bringing down Ian Blackford flies in the face of [SNP Dundee East MP] Stewart Hosie trying to pretend all is sweetness and light within the party, and is a clear sign of Nicola Sturgeon’s waning influence on SNP MPs.
‘Policy and personal disagreements are emerging all the time as the party’s reputation for iron discipline under Nicola Sturgeon disintegrates.’
Following Mr Blackford’s resignation as leader last week, Miss Sturgeon insisted there had not been a coup, despite reports that a group nicknamed the ‘Tuesday Club’ had plotted a challenge by Mr Flynn.
On the new leader’s second full day in the post yesterday, Mr Wishart, the Nationalist MP for Perth and North Perthshire, announced he was quitting his role as the SNP’s spokesman on the environment, food and rural affairs.
It is the first time he has moved to the party’s back benches in his 21 years as an MP.
In his resignation letter to Mr Flynn, he also made clear that he believed the Aberdeen South MP had plotted a challenge against Mr Blackford. He said: ‘We never had an opportunity to discuss your plans for the group, neither when you were canvassing opinion for a leadership challenge, nor at any point during the very short campaign for the leadership itself.’
In an attack on Mr Flynn, he said: ‘I remain bemused as to the reasons why you felt it was necessary to seek a change in our leadership, particularly when we see yesterday’s opinion poll, which shows support for independence at a near all-time high and support for the SNP at Westminster at an unprecedented 51 per cent. Usually change of this significance accompanies failure, whereas we are looking only at sustained and growing success as a movement and party.’
He said he believes plans to ‘reset the relationship with colleagues in government and in the Scottish parliament’ are ‘extremely important for the general culture within the party’.
Mr Wishart added: ‘The Westminster group is unique in the respect that we are a party of power in a parliament, in which that power can never be exercised. Many of us carry the scars following the many attempts to manage that unfortunate tension over the course of the years.’
Asked yesterday lunchtime about Mr Wishart’s claim that Mr Flynn had been canvassing opinion for a challenge, Miss Sturgeon said: ‘Forgive me, I’ve not read Pete’s letter yet.
‘I’m aware he has written a letter, I’ve not had the opportunity to read it yet because I’ve been doing other things.’ Pressed on whether she still believed that there had been no attempt to oust Mr Blackford, she said: ‘Ian stood down last week, the group elected a new leader earlier this week.’
Mr McDonald, MP for Glasgow South, did not give a reason in his resignation letter for his decision to leave his role as defence spokesman. He insisted that Mr Flynn and his deputy Mhairi Black ‘have my full and unequivocal support’.
Replying to Mr Wishart’s resignation on social media, Mr Flynn said: ‘Pete, thank you for your exemplary service for the SNP on the front bench in Westminster over so many years.
Source: Daily Mail