Extra loans will be given to the place of worship which has been battling cash flow issues since at least July 2016.
The problems were revealed as the Dean of the cathedral, Very Rev Charles Taylor, announced he was standing down.
At his retirement service he alluded that it was not his decision to leave.
He said that he had not made a comment about his leaving but "some have alleged that the manner in which it was effected was legally dubious, morally reprehensible, and pastorally disgraceful".
He added: "Well, they might care to think that. I could not possibly comment."
After he announced he was leaving the Bishop of Peterborough, Rt Rev Donald Allister, announced he was investigating the financial management and governance of the Cathedral.
The Bishop said: "The Cathedral is going through a cash flow crisis. It is taking too long to pay some bills, and paying the staff at the end of the month has been a close thing twice recently."
The Church of England's representative in parliament was quizzed on the situation by the MP Michael Fabricant. He asked Caroline Spelman what assessment the Church had made on the "appropriateness of procedures and practice" at the Cathedral.
She replied that there was "no reason to review the appropriateness of procedures and practice relating to the resignation".
The Church Commissioners, she said, were increasing the financial support they were giving the cathedral amid the crisis.
