Tax officers had previously questioned the process with which the south-coast club went into voluntary administration last month - a move that prevented them from being wound up.
"Despite HMRC continuing to have a number of remaining questions and concerns around the relationships of various parties, and a lack of detail of financial affairs, HMRC has now advised the administrators that we will no longer challenge the validity of the administrator's appointment," a statement from HM Revenue and Customs said.
"This comes in light of the additional material now provided following the judge's directions of 2 March 2010."
The league's bottom side, who became the first Premier League club to enter administration, axed 85 jobs on Wednesday amid debts of around 78 million pounds.
They could face a nine-point penalty deduction by the Premier League now that the administration process has been accepted, a punishment that would almost certainly result in relegation.
"HMRC would expect that now that the issue of validity is no longer in question, the administrator will be able to make early and real progress with the administration in order to get the best and most equitable return for all creditors," the statement added.
