The Scottish Islamic Foundation (SIF) has written to Lord Advocate Elish Angiolini querying the decision to prosecute Neil MacGregor for a breach of the peace, not terrorism offences.
MacGregor, 35, has admitted threatening to blow up Scotland’s biggest mosque and to behead one Muslim a week until every mosque was shut down.
He will be sentenced at Glasgow Sheriff Court on Friday.
“There has been criticism for the lack of exposure this case has got, but this stems from how the case was originally handled,” SIF chief executive Osama Saeed said. “Had he been a Muslim, we suspect that counter-terror police would have been involved from the outset, and it would have been processed in a completely different manner.”
Mr Saeed drew a parallel with the case of Mohammed Atif Siddique, a student from Alva, Clackmannanshire, who was jailed for eight years for internet-related terrorist crimes.
“No-one seems to have looked into the internet habits that radicalised MacGregor to take copycat revenge for (British hostage] Ken Bigley’s assassination in Iraq,” he said.
“We can be sure if he had been Muslim and had been inspired to replicate it, the result would have been quite different.”
Mr Saeed insisted he was not seeking to minimise the seriousness of Islamic terrorism cases.
“All we are calling for is consistency, and the authorities have to explain why the heavy books of the Terrorism Acts were not thrown at MacGregor,” he said.
“Islamic and far-right extremism are stablemates when it comes to violence – a toxic mix of ideology and grievance. We hear glib assurances that far-right extremism is being dealt with, but the evidence says otherwise.”
The SIF was founded last year, describing itself as a “platform for action”, and has received £400,000 from the Scottish Government.
Mr Saeed said the federation would request evidence from the case to be released under Freedom of Information laws.
An earlier hearing was told MacGregor admitted sending an e-mail to Strathclyde Police, threatening to blow up Glasgow Central Mosque if certain demands were not met.
Included in the message was a threat to behead one Muslim a week, in the same manner that construction worker Mr Bigley was killed after he was kidnapped in Iraq in 2004.
The court heard MacGregor, from Derbyshire, followed that e-mail with a 999 call to police on 5 February, 2007, in which he claimed he was from the National Front and that a bomb was going to go off at Glasgow’s Central Mosque.
Police searched the building for explosive devices, but failed to find anything suspicious.
In his e-mail, MacGregor wrote: “I’m a proud racist and National Front member. We as an organisation have decided to deal with the current threat from Muslims in our own British way like our proud ancestors.
“Our demands are very small. Close all mosques in Scotland, we see this is very easy – even you guys can handle that.”
He then wrote: “If our demands aren’t met by next Friday we’ll kidnap one Muslim and execute him or her on the internet, just like they did to our Ken Bigley.”
A Crown Office spokesman said that MacGregor was indicted on a charge of breach of the peace, aggravated by racial hatred, “following full and careful consideration of all the facts and circumstances in this case”.