The UK Treasury has said it will honour all of the UK's debt A vote for Scottish independence would delay the UK's return to triple A credit status, according to the ratings agency, Fitch.
A report by the agency suggested a Yes vote would hold "moderate risks" for the rest of the UK.
The agency said there would be a "one off" increase in the UK's debt if Scotland left the UK.
It also suggested some financial institutions could relocate to London, raising the UK's exposure to bank debt.
In its report, Fitch said it assumed a No vote in September's referendum, based on current polls, but a Yes vote would mean it would review the UK's credit rating.
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Colletta Smith BBC Scotland Economics Correspondent It has been more than a year since the UK lost its AAA credit rating and although the government have downplayed the significance of ratings, the prospect of waiting longer before getting the top rating back will not delight anyone in the Treasury.
Fitch had said before that Scottish independence was unlikely to impact the UK credit rating, but recent developments have changed their mind.
Today's report focuses on UK debt and its impact on the credit rating.
They say that the commitment the UK government made in January to honour all the debt already issued - even the chunk that an independent Scotland would take on - would bump up the UK's debt to GDP ratio.
Fitch say that would delay the possibility of the UK getting its AAA credit rating back again, because having a bigger debt burden is seen as more risky.
That's a concern for the UK government because when ratings agencies like Fitch lower their ratings, investors see it as a more risky loan, so countries have to pay more in interest.
The agency's report said there would be moderate risks in the areas of public debt, external finances, currency arrangements and the financial sector.The Scottish government has said that, if voters back Yes in September's independence referendum, it regards 24 March 2016 to be "a realistic independence date".
The report said Fitch expected the transition to independence "would be managed carefully, avoiding financial dislocations."
The report added: "If not, the pressure on the ratings would be greater."
Fitch said the UK's government's undertaking to honour all of the UK's debt would lead to "a one-off increase of 9.5% of GDP" in the UK debt ratio if Scotland became independent in 2016.
"We assume Scotland would gradually repay its loan to the UK," the report said.
"However, it would be illiquid and leave the UK exposed to Scottish credit risk, at least in the early years of independence."
Fitch said independence would "likely be mildly negative for the UK's balance of payments" as the UK would lose most of its oil export receipts to Scotland.
The report said that all of the possible currency options, "from a pegged or free-floating currency to a currency union", would pose risks to the remaining UK, including "competitive devaluation".
The agency added that some financial institutions could move their headquarters to London in the event of independence, which would "expand the size of the UK banking sector from an already high level of 492% of GDP; it would also increase cross-border and potentially cross-currency exposure".
In a previous assessment in 2012 the agency had concluded that Scottish independence would be likely to be neutral for the UK's credit rating, but said it had revised its view as it could no longer assume there would be "no impact on gross public debt".
The new report cautioned that Fitch would expect that a compromise could be reached between Scotland and the rest of the UK in any transitional negotiations.
"It would be in the best economic interests of the UK to ensure that an independent Scotland was, in the broadest terms, 'a success'", it said.
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