A copy of the letter is among more than 60 pages of documents provided to the Otago Daily Times yesterday, and which the newspaper believes are genuine.
Some of the material raises the question being asked widely in public in the wake of the fraud convictions.
"Why did they employ Swann anyway?" a lawyer is recorded in the documents as asking.
The accountants described in their July 1998 warning letter to the then Healthcare Otago - shortly after Swann was employed by the health provider - how they believed he had a "criminal intent".
They claimed they were "both in a position to clearly substantiate the comments that have been made".
Both signatories were contacted yesterday but declined to be interviewed.
Swann and business associate Kerry Harford are in jail on remand awaiting sentencing for their six-year invoicing scam.
The letter's whereabouts and its disclosure have been a source of irritation, frustration and now concern for the health board.
It could not locate its copy of the letter, which had been addressed to former chairman Ross Black and dated July 13, 1998.
Mr Black said on Sunday he had immediately acted on the letter, handing it to the board's acting chief executive for investigation.
Mr Black contacted the ODT again last night and said he did not say, as published yesterday, that he had been warned by two businessmen that they had had "bad experiences" with Swann, but in fact said he had been told of instances of "dishonesty" in Swann's previous employment.
The newspaper accepts this is what Mr Black said.
Mr Black also wanted to clarify that legal advice to the acting chief executive at the time was that it could not use unsubstantiated and unproven allegations to review a person's employment.
In 2006, the SFO refused the health board's request to make the letter public following an Official Information Act request by the Otago Daily Times, in December of that year.
It is believed but yet to be confirmed that a second, separate, warning letter from a Dunedin-based businessman was delivered to the board about the same time as the first.
While board chairman Richard Thomson wanted the July 1998 warning letter released, its existence raises questions about who knew what about Swann at the time, and the ramifications that knowledge may have on the yet to be determined ODHB insurance claim for up to $5 million for its losses.
An electronic copy of the accountants' letter was sent to SFO investigator Roger Small by one of the signatories on November 13, 2006, about two weeks after the board lodged its civil claim against Swann and 19 other defendants and about eight months before the SFO would lay its own, separate, criminal charges.
It is SFO policy not to respond to questions on individual cases.
The documents also disclose for the first time the then Minister of Health, Pete Hodgson, is identified as having received a copy of the accountants' warning letter.
An email from legal counsel directed to senior ODHB management and SFO investigators on November 24 (11 days after the warning letter was emailed to the SFO) states: "The minister already has a copy of it and needs to be briefed as to its release in order to deal with the inevitable questions in the House, and we need to strategise for the publicity that will ensue.
"Because as soon as the letter is in the public domain, the next questions will be: who received it, what did they do with it, why did they employ Swann?"Mr Hodgson said yesterday he was made aware of the existence of the letter in September 2006 by Mr Thomson, before the board went public about the frauds.
However, he did not have a copy or know its exact details, other than that "the letter was a smoking gun, but not enough evidence".
On November 14, 2006, Mr Hodgson told the ODT: "The Otago health board's actions and sequence of events to date has been commendable".
The 60 pages of documents contain numerous emails, memos, minutes and financial documents collated or sent by the SFO, Audit New Zealand, Healthcare Otago, the ODHB and legal counsel, including a brief report on an informant's activities overseas.
No formal complaints were apparently made or charges laid against Swann in connection with earlier business dealings.
None of Swann's former business associates have agreed to be interviewed.
They include members of some of Otago's most prominent business families.
