Mr Russell insisted the remark was only meant as a joke as he appeared before Holyrood's constitution committee today where he was giving evidence on the implications of the Brexit deal for Scotland.
The SNP minister was addressing the prospect of a "No Deal" Brexit scenario and was told by Tory MSP Murdo Fraser that the Prime Minister's deal would be a better option.
"The reality of this situation is that both are very bad."
Mr Fraser suggested a no deal scenario was "less likely than alien invasion."
But Mr Russell hit back: "Oh, I don't know - have you seen Jacob Rees-Mogg?"
The remark prompted calls from the Tory MSP to "elevate the discussion" before another Tory Adam Tomkins, later said Holyrood Presiding Officer Ken Macintosh had called for respect to be shown to Parliamentarians across the UK.
The SNP minister insisted that the blood "did not rush to my head."
But he added; "If my joke misfired in any sense, then of course I'm sorry about that."