The Sunday Times newspaper has questioned the use of almost £2m of Libor fine funds handed to the three veterans charities.
The charities were among those to receive grants from the funds, which came from the fines levied on banks after the Libor rate-rigging scandal.
This morning, two of the charities defended their use of the funds and said they were disappointed with the coverage.
The article raised questions over some of the techniques used to help armed forces veterans and claimed funds had been given out with a lack of checks and balances.
It questioned the use of £933,000 of funds given to the Warrior Programme, which used techniques including "time-line therapy" and neurolinguistic programming, which it said psychiatrists had claimed were unproven.
The Warrior Programme said in a statement that it was disappointed the article "failed to recognise the evidence the Warrior Programme has generated and the continual evaluation we are undertaking".
It said its work funded by the Libor grant was "meticulously accounted for and the funding team received detailed progress reports".
It said: "We delivered the project outcomes within budget and were complimented on the success of the project."
The Sunday Times article also highlighted the use of £414,000 of funds given to Veterans Outreach Support and claimed that the charity spent much of it on giving veterans craniosacral therapy, which the article said was a technique "deemed worthless by medics".
But the charity said today that only about £9,000 of the £414,000 grant was spent on a trial of craniosacral therapy.
It said the trial was run in response to overwhelming anecdotal evidence from service users, but proved inconclusive and came to an end in April 2015.
The Portsmouth-based charity, which runs a monthly drop-in service that is attended by more than 500 people a year, said it employed an in-house clinical team of mental health experts and offered only therapies that were approved by the National Institute for Health and Care Excellence.
The Sunday Times article also highlighted about £500,000 of Libor fine money that went to a charity called the Veterans Council, which promised a one-stop shop for veterans that did not exist, the paper claimed.
The charity’s website was under construction and its phone lines appeared to be non-operational on Monday morning.
A Charity Commission spokeswoman was unable on Monday morning to comment on whether it had any concerns about the claims.