Apart from HMRC, Portsmouth's creditors have voted overwhelmingly - by 81.3% - in favour of a deal which would see the club exit administration and avoid any points deduction in the npower Championship next season.
HMRC, who oppose the Company Voluntary Arrangement (CVA) which will see non football creditors receive only 20p for every pound they are owed, are not backing down.
They have 28 days to appeal but it is understood they are keen to avoid a court fight against Portsmouth's administrators.
HMRC said in a statement: "HMRC notes that the result of today's vote was to accept the CVA proposals. We will now be carefully considering our position.
"HMRC stands by the full amount of its claim. We will now carefully consider our position following chairman's decision to reduce the amount of our claim for voting purposes."
HMRC are challenging the Premier League and Football League's rule that 'football creditors' get priority in having their debts paid off first and in full.
The statement added: "HMRC believes the so called "football creditors rule" is unfair, unlawful and unacceptable.
"It cannot be right for millions of pounds worth of assets and income of Portsmouth FC to be earmarked for payment of football debts in full while other creditors - including the public purse - have been offered a mere 20p in the pound over five years."
Andrew Andronikou, the man appointed by an insolvency court to be Pompey's administrator, only gave HMRC voting rights for £24million debt rather than £37million, in effect preventing them from blocking the CVA vote which needed 75% of creditors in favour.
He claims the other money relates to image rights and should be not be considered part of the club's debts.
Andronikou told a meeting of creditors today that the CVA had been "duly approved".
Nigel Tresidder, chairman of the Pompey Supporters' Club central branch, attended the meeting and said he was buoyed by the outcome but concerned about the continuing uncertainty.
He said: "It's excellent news other than HMRC have 28 days to appeal against it.
"I think the people in charge of the club are confident of winning any appeal but it's time the uncertainty came to an end."