Mr Swire had submitted two claims for the same bill, in July and October 2007, but had raised his concerns with the Fees Office at the time whether it had already been submitted, only to be told everything was in order.
It has now been established that Mr Swire was wrongly paid twice and he has refunded the money.
There is no suggestion that he deliberately made a double claim.
In a letter to Mr Swire, the Fees Office confirmed that he asked them in October 2007 “to check his ACA payments in order to determine whether this bill had been previously submitted”.
“This check was not carried out with enough rigour and therefore the bill was indeed, and in error, paid a second time.
“I apologise that we did not notice this at the time and also apologise for the difficulties this has caused you.”
Mr Swire said: “This is an error by the Fees Office, because at the time I raised my concerns, not once but twice. There are lessons to be learned.
“The Fees Office have had an incredibly difficult time.”
But he added: “It’s quite clear this shows MPs have at times been let down by the Fees Office.”