Joanna Cherry said it is "remarkable" Peter Murrell's SNP membership has not been suspended and said his treatment had been "very different" to other members of the party.
Cherry compared the case of the former party chief executive and Nicola Sturgeon's husband to MSP Michelle Thomson, who was suspended in 2015 over a police probe.
Cherry also said "gender crticial" feminists had been suspended by the party for their tweets.
The SNP is in crisis over a police investigation into how around £600,000 of indyref2 donations were spent.
Murrell was arrested last week as part of the investigation. He and Sturgeon's home was searched over two days, as was the SNP headquarters in Edinburgh.
H was released without charge after 11 hours of questioning as enquiries continue. He has not been suspended by the party.
Cherry tweeted on Tuesday evening: "Of course Murrell is innocent until proven guilty but the decision not to suspend his party membership given the whole circumstances is remarkable and very different to treatment of Michelle Thomson and others including feminists suspended for gender critical tweets."
Falkirk East MSP Thomson was suspended by the party when she was an MP after police looked into "alleged irregularities" related to property dealings. The transactions caused her solicitor to be struck off.
Thomson denied any wrongdoing and criminal proceedings were never brought. She rejoined the SNP in 2018 and won her Scottish Parliament seat in 2021.
Thomson, who ran Kate Forbes' leadership campaign, said the SNP’s rules around the membership of those who were under criminal investigation were unclear.
She said: “He (Peter Murrell) is innocent until proven guilty. He has not been charged with a crime.
“That may change, but we need to be clear about what specifically are the rules.
“I’m certainly not clear about that and I’ll be asking about what the position is.”
This comes after it emerged the SNP's auditors quit in October but the public were not told.
The Herald also revealed that Johnston Carmichael stopped working as auditors for the SNP's separate Westminster group at the same time.
The Westminster Group had an income of £1.5m in 2021 and runs research and staff budgets for the party's 45 MPs.
It is yet to appoint new auditors.
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