The SNP’s Westminster leader Stephen Flynn has said MPs cannot “pick and choose” when they take the party whip after Angus MacNeil’s membership was suspended.

The Na h-Eileanan an Iar (Western Isles) MP, who has sat in the Commons since 2005, announced last week he would not re-join the SNP Westminster group following the end of a suspension levied against him after a reported bust-up with the group’s chief whip, Brendan O’Hara.

In a letter to Westminster leader Mr Flynn, Mr MacNeil hit out at the party’s strategy for achieving its central aim of Scottish independence, saying the SNP was “utterly clueless” on the issue and that he would not return to the group until at least after the party’s October conference.

But within days Mr MacNeil was suspended from the party.

Speaking to BBC Radio Scotland’s Good Morning Scotland programme, Mr Flynn said: “In relation to Angus’ position, I think it’s well versed in the public domain that Angus chose not to return to the SNP whip.

“You don’t get to pick and choose, no matter which party you’re in – when and if you hold the party whip, if you’re a member of the party you should be holding the party whip.”

It is now for the party to determine if Mr MacNeil, who had been a frequent critic of the party’s leadership in recent years before his suspension, will be able to return, Mr Flynn said, refusing to weigh in for fear of “influencing that process”.

But the Westminster leader played down any assumptions of a personal rift between him and Mr MacNeil, saying: “I don’t have any personal animosity towards Angus at all, as I’m sure he would testify to.

“I think he’s a very colourful and lively character and a strong advocate for Scottish independence.”