First Minister John Swinney, who appointed Murrell in 2001 during his first spell as SNP leader, has apologised to party members.
However, he has denied any attempts to shut down concerns about party finances.
The SNP leader said he was “horrified” by Murrell’s conduct, describing it as an “overwhelming betrayal”.
He has repeatedly rejected calls for an inquiry into the case, saying it would not provide more answers than the four-year police investigation.
Murrell’s lawyer confirmed his client’s intention to pay back the sum embezzled, with a proceeds of crime hearing scheduled for 14 September.
The exact amount prosecutors are seeking is yet to be made public and will be adjusted for inflation. Those funds would be handed back to the state, which spent millions on the police investigation.
Separately, the SNP is hoping to recover £400,000 from Murrell through a compensation order.
After Murrell was sentenced, Swinney said he would not be visiting him in prison.
The first minister has indicated that he still does not understand why the former SNP chief executive stole £400,000 from the party.
Asked if he could forgive Murrell, Swinney said that as a matter of his faith he does not believe people should pay for their crimes forever.