Deputy First Minister Shona Robison warned the SNP will be expected to get its act together as Tory leader Rishi Sunak mocked the party’s escalating troubles.
Humza Yousaf’s No2, who is also finance chief, admitted it is “frustrating” her party is being undermined by the financial row.
SNP treasurer and Mildlothian MSP Colin Beattie was arrested on Tuesday, nearly two weeks after Nicola Sturgeon’s husband and ex-chief executive Peter Murrell was taken questioned under caution.
It comes as police continue to investigate the spending of more than £600,000 donated to the party for independence campaigning.
Tories fined twice
Prime Minister Mr Sunak claimed the SNP is distracted from governing because of the probe and said Ms Sturgeon had left both her party and country in a “mess”.
He said: “What we’re doing is not getting distracted by things going on elsewhere. We’re just going to motor on with the job.”
However, Dundee-born SNP Westminster chief Stephen Flynn said his party would take “no lectures” from the Tories.
Hitting back at the Conservative leader, he reminded the House of Commons Mr Sunak has been fined twice by police.
He also took aim at reports the Scottish Tories will encourage unionist voters to back Labour north of the border to oust the SNP from key seats.
Mr Sunak and Mr Flynn were met by choruses of cheers and boos as they clashed at the first Prime Minister’s Questions since before Easter.
Despite Mr Flynn going on the attack, Holyrood deputy Ms Robison admitted voters want to see the SNP “gets its own house in order”.
During a visit to Glasgow, she told journalists: “Of course it is frustrating that we are not able to talk as much as we would like about the priorities that were set out yesterday.
“Although the public will expect the SNP to get its own house in order, they also expect us as a Government to help their households with the cost-of-living pressures.”
Mr Beattie’s arrest came just hours before Mr Yousaf announced he was delaying or pausing several big policy initiatives introduced while Ms Sturgeon was in power.
In Holyrood, the first minister admitted he was “surprised” that one of his party’s backbenchers had been taken in for questioning by police.
Doubts have been raised over whether Mr Beattie can continue to sit on the Scottish Parliament’s public audit committee.
Mr Yousaf has faced demands to remove him from his role and a substitute from the SNP will attend in his place on Thursday.
Ms Robison said: “Colin Beattie’s a very decent guy, and he will recognise that some of these issues are going to be challenging over the next period of time.”
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