Mr Justice Norris approved an application by directors at a High Court hearing in London after being told that the Championship club owed millions of pounds.
He said he was satisfied that Portsmouth was insolvent and hoped that the appointment of financial experts to manage affairs would allow the club to "stagger on" until a new buyer could be found.
The High Court appointed PKF as administrators, overlooking Hacker Young who had previously undertaken the role for Portsmouth.
Her Majesty's Revenue & Customs welcomed that decision.
"HMRC is pleased that the court agreed with our view that the creditors of any business have a right to expect that the administrator in these circumstances is completely independent," a statement from HMRC read.
"HMRC felt strongly that the appointment of Hacker Young as administrators to Portsmouth FC, whilst at the same time being administrators for the parent company CSI and its previous roles with the various Portsmouth Football Clubs, would present issues of conflict.
"This is why we suggested the appointment of PKF whose knowledge of the football industry and lack of previous connections to Portsmouth FC should reassure creditors."
The judge heard that the club had an unpaid tax bill of about £2 million and owed about the same to other creditors.
He said he thought that creditors would get a better deal if the club was placed into administration rather than liquidated.
Lawyers told the hearing that being placed in administration could result in Portsmouth being docked more than 10 points by the Football League - a penalty that could suck the club into a relegation fight.
But outside court accountant Trevor Birch, whose team will manage administration, said he hoped that a new owner could be found and urged fans to "keep the faith".
Portsmouth directors said earlier this week that the club had applied to go into administration.
The club's parent company, Convers Sports Initiatives, went into administration in November.
Two years ago, Portsmouth became the first Premier League club to enter administration.
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