Administrators wanted the club to pay back 20 per cent of their debts under a company voluntary agreement (CVA), but HMRC want more of the club's unpaid £13million tax bill to be settled.
Under Premier League and Football League rules, football creditors must be paid in full - this includes clubs owed transfer fees and players owed wages - but there is no such protection for other creditors, even HMRC.
"We are acting in the interests of all those creditors who are not in the football industry. We don't think it's right that they are offered 20p in the pound against full repayment for [football creditors]," an HMRC spokesman told BBC Sport.
Pompey are unable to sign players until they come out of administration, and this appeal means that could now be as late as November. It will almost certainly come after the transfer deadline day in August.
It also raises the possibility of the Football League imposing a points deduction for starting the season in administration, instantly throwing the club into a battle to avoid relegation to League One.
The Burnley winger Chris Eagles has turned down a move to the Scottish Premier League champions Rangers.
Eagles, 24, held talks with the Scottish champions on Wednesday and the Clarets accepted an offer - which they describe as substantial for him on Thursday morning.
Laws said they still hope to keep him and that accepting the offer should not be seen as a desire to sell.
Eagles has made 95 appearances for Burnley since joining from Manchester United two seasons ago.
Burnley expect to complete the signing of a goalkeeper on a season-long loan this week. Brian Laws, the Clarets manager, will not reveal the name but Clarets MAD are confident it is Newcastle United's Fraser Forster.
The Reading manager Brian McDermott has told Scott Davies and David Mooney that they can leave the Madejski Stadium.
The pair have been left in England while the first-team's pre-season preparations continue in Slovakia and Croatia.
The Derby County striker Steve Davies has suffered cruciate ligament damage in training and will miss the start of the season.