Owen Thompson has been replaced as the party’s chief whip at Westminster in a surprise first move by Mr Flynn as he overhauls the group’s front bench in the Commons. Replacement Martin Docherty-Hughes, the West Dunbartonshire MP, has instead been given the role.
The move comes as Mr Flynn sent an email to SNP MPs, confirming he was putting together a “new-look team” over coming days as he seeks to stamp his authority and initiate a tactical shift at Westminster.
The change was confirmed as Pete Wishart, the SNP’s MP for Perth and North Perthshire, announced his resignation from the party’s front bench in a critical letter.
Mr Wishart, who was first elected to Westminster in 2001, has resigned as the group’s DEFRA spokesman.
In the letter, Mr Wishart said: “We have 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.
"I note that you hope to bring positive change to the way the group is run and that you wish to reset the relationship with colleagues in Government and the Scottish Parliament … 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. I am sure that this is something that will become apparent to me during the course of your leadership.
“I also look forward to learning first-hand what you hope to do differently in the day-to-day management of the group.”
However, the Perth and Perthshire North MP said Mr Flynn had his “full support”, adding “I remain at your service if you do wish to make use of my experience in the Westminster group.”
Responding to the letter, Mr Flynn thanked Mr Wishart for his “exemplary service” on the SNP front bench.
He added: “As ever, my door remains open and I look forward to working with you as we support colleagues in Holyrood, hold the Tories to account, and work to deliver independence.”