Reports in Australia say that it could knock as much as Â£200m (A$425m) off its value.
The parent company of the bank plans to float the Glasgow-based lender in Australia later this year.
Chancellor George Osborne announced he was phasing out the bank levy.
He also announced plans to introduce an 8% surcharge on bank profits, in addition to corporation tax.
That knocked share prices of smaller UK banks which are already traded.
A bank analyst at the Commonwealth Bank of Australia calculated that would knock A$425m off its valuation, and suggested that could push National Australia Bank (NAB) to sell off a larger stake in order to meet its target for raising capital.
A spokesman for the NAB was reported by the Melbourne Herald Sun saying the move would have no impact on the parent bank's earnings.
A spokesman in Glasgow for Clydesdale Bank, which includes the Yorkshire Bank brand, declined to comment.
Clydesdale Bank is seen at the Melbourne headquarters and in the Australian media as a drag on NAB, having amassed a large portfolio of bad property loans, and the high costs of redress for mis-selling financial products.
The new NAB chief executive, Andrew Thorburn, has made it a priority to split Clydesdale, handing up to 80% of it to NAB investors and selling the remainder on London and Australian exchanges.
Earlier this week, senior staff at NAB in Melbourne set out the case for investing in the spun-off UK bank, to institutional investors in Australia.
They portrayed it as one of the so-called challenger banks which is best placed to take on the British market's 'big five'.

Dover rise to third while Wrexham are now six points off the top five after Ricky Modeste's second half winner proved decisive in a tense contest.
Modeste fired home off the post after Sam Magri's effort in a game low on quality chances.
James Gray hit the crossbar as Wrexham pushed for an equaliser, while Simon Heslop also came close.
Wrexham manager Gary Mills told BBC Radio Wales: "It's a disappointing day for us and we never really got going. I've said to the players that there's no point in us looking at that now, the final whistle's gone.
"We've got four games left . It's tougher but still doable and we've got to win on Tuesday at Guiseley.
"If we win on Tuesday then we got to Tranmere to beat them to go above them and that's as simple as it is. We battle on."

Denmark international Fischer, 21, has been with the Amsterdam club since 2011 and scored 24 goals in 79 league games.
The forward visited Boro, who were promoted to the Premier League this season, for a medical and agreed terms.
"It's the greatest league in the world and I feel really ready," Fischer told Danish TV station TV2.
Eight-times capped Fischer has agreed a three-year deal.
Fischer emerged as a key player at Ajax under recently departed coach Frank De Boer, alongside compatriots Lasse Schone and Christian Eriksen - the latter whom he will play against in next season's top flight when Boro face Tottenham Hotspur.
The surcharge tax on bank profits announced in the Budget is being seen as another blow for the sale of Clydesdale Bank.
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Dover maintained their National League promotion push at the expense of Wrexham at the Racecourse Stadium.
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Ajax winger Viktor Fischer will join Middlesbrough for around £3.8m at the start of the international transfer window next month, BBC Tees reports.