The revolt is highly awkward for Prime Minister David Cameron, who has promised to protect the Barnett Formula, which sees Scots get £1,300 a year more per head than the English in public spending, as part of further powers for Scotland if voters choose to stay part of the United Kingdom.
Perry said that pledge issued by the main three Westminster parties to maintain current level of funding for Scotland and devolve local taxes is "hardly equitable" to those in England.
The Tory MP, an ally of George Osborne who was promoted to be rail minister in July's reshuffle, said that the government must not offer "financial party bags to appease Mr Salmond".
Writing in the Wiltshire Gazette and Herald, she predicted that Parliament would be recalled next week to "understand the result" of the referendum.
Perry expressed fears that “a whole raft of goodies on offer for Scotland that will be paid for by us south of the border to try and appease the Yes voters".
The Tory rail minister also warned that the UK government does not have any plans in place for the rail industry in the event of a "Yes" vote.
She told Rail News: "There is no contingency plan. There might be some secret proposals in a box somewhere, I suppose, but if there are I haven't seen them."
Perry's intervention makes her the first government minister to back the potential Tory revolt in the event that Scots reject independence.
Tory MP James Gray, a former Shadow Scottish secretary, told the Telegraph: "Talk about feeding an addiction. The more you give them, the more they want, and we would be back with calls for independence within a decade or sooner."
"For too long the rights of 55 million English have been subordinated to the shouting of 4.5 million Scots. That must end."
Tory MP Philip Davies said on Twitter that he would not be voting to maintain an "unfair funding settlement for Scotland". He also said he would do as much as possible to stop Scottish MPs voting on issues in Parliament that do not relate to Scotland.
In the event of a No vote, I will be doing all I can to stop MPs from Scotland voting on issues in Parliament which don't relate to Scotland— Philip Davies (@PhilipDaviesMP) September 16, 2014
Davies' call was endorsed by former Tory deputy chairman Lord Ashcroft, who said it was "hard to argue" with his position.
In a hint about his views, the Tory peer earlier posted a link to an article that argued more powers for Scotland should see an "end" to the Barnett Formula and "self-government" for the English.
More devo for Scotland must mean an end to Barnett and self-government for England. http://t.co/eiIHYLmnPw— Lord Ashcroft (@LordAshcroft) September 16, 2014
Meanwhile, Tory MP Mark Pritchard said it was "time to discuss" a new settlement that must be "fair" for "the whole of the UK".
Time to discuss new Settlement, for the whole of the UK, is for later not for today & those discussions must be fair, equitable & pro Union— Mark Pritchard (@MPritchardMP) September 17, 2014
The position was backed by senior Tory MP John Redwood, who said that England "needs a voice" after the independence referendum.
A Yes vote will hardly be easier for Cameron, as Tory MPs have signalled that they would oust him as Tory leader if Scots voted for independence.