Humza Yousaf was surprised to receive the request to speak against his party's flagship policy of Scottish independence.
The case of mistaken identity follows a difficult few weeks for Better Together.
The organisation has been accused of dogged negativity and faced complaints from pro-Union sources that it is running an uninspiring campaign. In an email from Better Together, Mr Yousaf was asked if he could speak at an event organised by BEMIS Scotland, the national umbrella body supporting the development of the ethnic minorities voluntary sector in Scotland, in August.
Mr Yousaf, the Scottish Government's external affairs minister, accused his opponents of being "shambolic". And he revealed that he would be taking part in the debate, organised as part of Edinburgh's JustFestival - speaking against Better Together.
Mr Yousaf said: "With gaffes like this, it's no wonder the No campaign are in such deep, deep trouble.
"They are a shambolic campaign who are dropping in the opinion polls - they don't have their finger on the pulse of Scotland, and this latest blunder proves it.
"While I look forward to speaking at the event, it will not be for the No campaign, but to outline the many benefits of an independent Scotland."
A Better Together spokesman brushed off claims of a gaffe and called on the First Minister to represent the No campaign at the debate.