The new debt relates to a period of unpaid tax in August before the new owners, led by chairman Ilyas Khan, came to the club.
Club president Peter Marsden is delighted to put the financial worries behind them and focus on events on the pitch, with Stanley currently mounting a surprise bid for the League Two play-offs.
"As of today (Thursday) we are the most up to date we have ever been in the history of the club in paying our tax," he told the Lancashire Telegraph. "I am sure that HMRC are delighted with everything the club has done to remedy this situation.
"We now go forward with certainty in our ability to meet our HMRC payments in the future. Now our tax blues are well and truly behind us we hope we can now focus on events on the pitch."