Dr John Kelly, of Edinburgh University, said legal affairs minister Annabelle Ewing had taken comments he made in 2011 “out of context” to give the impression he supports the Offensive Behaviour at Football Act.
Earlier this week, Celtic said it was “extremely disappointed” the government had used a six-year-old quote from its chief executive Peter Lawell in a “clear misrepresentation of (its) long-standing” opposition to the legislation.
Dr Kelly has written to MSPs to express his frustration at the minister’s “selective” use of his own comments to indicate his backing of legislation he has “never supported”.
Ms Ewing used the quote in a submission to Holyrood’s justice committee which is currently consulting on legislation which would repeal the 2012 Offensive Behaviour Act.
Opposition parties have united behind a bid by Labour’s James Kelly to scrap the legislation.
Dr Kelly said the Scottish Government had used a “snippet” from a BBC interview instead of drawing from a detailed submission he provided to MSPs which showed he had “serious reservations” about the bill.
He said: “For the record, my position on the bill has not changed from 2011. I thought it was a good thing the Scottish Government sought to introduce a bill that would protect people’s ethnic identities...but the protection of sectarian minority identities has not been protected. It’s the opposite: they’re trying to criminalise sectarian identities.
“It’s pretty clear to any semi-intelligent person from the minister's evidence that they have struggled to get support. They have used the words of a dead lawyer (Paul McBride QC) – I don’t know if they’ve used them out of context.
“Celtic have complained about the use of a quote that was a number of years old. They have certainly used my words out of context. They have misappropriated the meaning of the quote.”
Labour MSP James Kelly said: "This underlines just how desperate the SNP has been to defend a poorly drafted piece of legislation that has been branded mince by judges and has broken down trust between fans and police. They should apologise to Dr Kelly and withdraw his quote from their evidence submission.
"The reality is tackling sectarianism goes far beyond 90 minutes on a Saturday or 140 characters in a tweet. The Football Act was and remains an attempt by the SNP to posture about taking sectarianism seriously."
A Scottish Government spokeswoman said: “The quotes in the Scottish Government’s submission highlight there was support for the principle of legislation to tackle unacceptable conduct at football in 2011.
“We fully recognise that some of those quoted do not support the legislation as it has been implemented – this is clearly stated in the submission to ensure that no-one’s current position is misrepresented.”