In an email last year, enterprise minster Jim Mather said he “agreed on all counts” that the first minister’s strategy on promoting Scotland in the US was “potentially very damaging”.

Mather made his comment after a diaspora charity he helped to set up, The Scotland Funds (TSF), and which he described as “one of the best things I have done”, failed to receive core funding from the government. Emails also show that the minister was furious when he learned that a key Salmond adviser in the US, Alison Duncan, had set up a similar charity called the Scotland Foundation to woo wealthy expats.

A senior SNP source said: “These emails provides a fascinating insight into Jim Mather’s views. He is much closer to John Swinney than Salmond.”

TSF was established in 2004 to help raise money from the Scottish diaspora in the US and Canada.

Although established on a cross-party basis, with Tory MSP Murdo Fraser and former Labour member Gordon Jackson on the board, the charity had good links to the SNP. When Dick Mungin, chief executive of TSF, asked justice secretary Kenny MacAskill in August 2007 whether he could count on his support in receiving core funding, the Cabinet minister said in an email: “Sure can.”

Mather, who left the TSF board after becoming a minister, said in his resignation letter: “I view our joint founding of this great organisation as one of the best things I have done.” Emails obtained by this newspaper show that when the Scotland Foundation was being set up by Duncan, the Nationalists’ legal representative in the US, after the SNP election win, Mather and TSF viewed the situation with deep suspicion.

In one email, Mungin said to Mather: “I heard today that A Duncan is attending the Riding [an event marking the Scottish Parliament’s opening] as a guest of AS. I still believe there is potential for problems from that direction.”

The enterprise minister responded: “We will manage this.”

Emails from Mather to Duncan also reveal the minister’s anger about her new venture. “Frankly I am very disappointed that when, at our meeting, I mentioned the continuing momentum and traction of The Scotland Funds that you were unable to brief me on the fact that you are now embarked on a very similar project,” Mather said in one email.

“Indeed, you seem unable to mention its name in this latest email. Can you understand that this fuels disquiet?”

The Scotland Funds’ bid for core funding failed and a separate application for £12,000, to help organise diaspora events in Canada, was nearly rejected following what Mungin describes as an intervention from the first minister.

The next year witnessed the collapse of TSF and the rise of the Scotland Foundation, which has now received Internal Revenue Service (IRS) approval.

However, weeks before TSF announced its closure in autumn 2008, Mather aimed a blow at Salmond.

In an email to the enterprise minister, Mungin said of the first minister: “I believe that AS [Salmond] taking a line, regarding TSF and diaspora engagement, which is based on his attachment to Ms Duncan rather than the experience and work of one of his own ministers is potentially very damaging.”

In his reply, Mather stated: “Agreed on all counts.”

Asked to explain the email in which he criticised the first minister, Mather said yesterday: “It’s a long time ago and I was just doing lots of things at the time and just trying to crack on. There’s nobody more loyal to the first minister than me. You can dredge up more and more emails, but you are not going to get anything more out of me on this.”

Mungin said of the email: “Jim agreed with me that the first minister’s party attachment to Alison Duncan was not a good thing at all. “I’m pleased that the facts are now in the public domain but saddened that a narrow personal and political agenda triumphed over a visionary and

genuinely cross-party supported

charitable initiative.”

A spokesman for Alex Salmond said: “This is all ancient history – the reality is that Mr Mungin’s ambitions for The Scotland Funds were not delivered.”

Duncan did not return calls.