The Welsh Amateur Boxing Association (WABA) says the audit found no evidence of fraudulent activity,
But its chairman said it would take all the steps recommended to put things right.
Sports Wales said it would continue funding the association, but it had put special measures in place.
The report into the activities of the Welsh Amateur Boxing Association (WABA) was commissioned by the association, alongside the Welsh government and Sports Wales which oversees and promotes sport and advises the government.
The audit was carried out by accountancy firm, KTS Owens Thomas.
In their report, which has been published in a redacted form on WABA's website, the auditors said: "It is our view that in its current state WABA is not fit for purpose and does not qualify to receive public money.
"Sport Wales must consider the implications of this finding.
"We consider that with the implementation of the recommendations set out in this report, WABA will become fit for purpose and qualify to receive public money."
In 2012, WABA received grant support from Sports Wales of just over Â£190,000 - more than double its Â£89,000 grant in 2006.
The audit report lists a series of financial concerns:
The report also raises issues over the way the association has been run since becoming a limited company in 2003.
It noted: "Some members have expressed concern that WABA is not open to constructive challenge and there appears to be divisions in the membership.
"Overall, we have found corporate governance to be poor and dysfunctional. We consider that it is improving, but has not reached an acceptable level."
The auditors make 38 recommendations for the sporting body's future, including measures to tighten financial controls, banking systems, and expenses management.
Their report also calls on the board to "improve the culture at WABA", and to work with Sports Wales to ensure it follows an action plan to implement the recommendations.
'Simply not acceptable'
Responding to the report, WABA chairman Terry Smith told BBC Wales: "Obviously we are very disappointed, but we will take all the steps recommended to put things right as quickly as possible."
He said much of the organisation was run by unpaid volunteers who did not have formal financial training.
But he disputed some of the report's findings, including the issue of unsupported spending.
Sports Wales said WABA's failures were "simply not acceptable".
Chief executive, Sarah Powell, said an action plan was now in place to resolve the issues at WABA.
She added: "In the best interests of the sport's grass-roots participants and elite competitors, Sport Wales has decided to continue funding WABA, but has put in place special measures to protect public funds, until such time as satisfactory progress has been made on the recommendations."
The body responsible for amateur boxing in Wales is "not fit for purpose" and "does not qualify for public funding", an independent audit report says.