S&P said the new legislation was unexpected and could signal a "weakening of extraordinary state support for systemically important banks."
However, Spindelegger said that the draft law, which would transform Hypo Alpe Adria from a bank to a wind-down unit or "bad bank", had previously been flagged.
"This is not a surprise for anybody," he told CNBC. "We decided about this three months ago, in the Council of Ministers."
Spindelegger denied the law would set a precedent for investors footing the bill in other cases of bank failure.
"This is a very special case," he said. "No other bank is involved."
The proposals mean that 890 million euros ($1.21 billion) of subordinated debt in Hypo Alpe Adria will be wiped out, ensuring that Austrian taxpayers do not foot the entire cost of the bank's collapse.
According to press reports, the government will also seek an 800 million euro contribution from German lender Bayern Landesbank, which co-owned Hypo Alpe Adria before it fell into state hands.
However, subordinated debt guaranteed by the federal government is not expected to be wiped out.
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Back in February, RBS warned that Austria might not uphold Carinthia's state guarantee on Hypo Alpe Adria debt.
On Wednesday, RBS's Alberto Gallo said the overruling of state guarantees had negative implications for German as well as Austrian banks.
"The German Landesbanks also benefit from state guarantees," said the strategist in an RBS research note on Wednesday. "However, the Austrian government's bail-in proposal highlights the risk that these regional state guarantees may not always be upheld if a bank needs support from the national government."