Finance secretary Derek Mackay said the reductions were being held up by the need to get approval for continuing the current exemption for Highlands and Islands airports.
He accused the UK Government of placing "unacceptable conditions" on notifying the European Commission that Scotland planned to continue the exemption when it introduced a new, lower air tax next year.
However, Labour said the problem was "a convenient opportunity to kick a bad policy into the long grass".
The Conservatives said the SNP was trying to "cosy up" to the Greens to get its budget passed, which they have threatened to oppose over the tax cut.
The Scottish Government is due to replace UK-wide air passenger duty (APD) with its new air departure tax (ADT) next April.
It plans to halve the current APD rates of Â£13 per passenger on shorter flights and Â£78 for trips over 2,000 miles.
However, the timing of the cut is now in doubt because of the need to win European Commission approval to continue the Highlands exemption under the new tax, which has been in force since 2001.
The Scottish Government said transferring the exemption to ADT required "notification to and assessment by the commission under state aid rules, in compliance with EU law."
Mr Mackay told MSPs he had an alternative proposal, using tax rates and bands, which would "provide the same benefit for all Highlands and Islands flights including connecting flights".
However, he said the UK Government had suggested delaying the transfer of the tax indefinitely in the absence of a solution.
Mr Mackay said: “To match the exemption for all Highland and Island flights including connecting flights would require the Scottish Government to forego annual revenues of more than Â£320m.
“I have suggested that the UK Government agrees to amend the Block Grant Adjustment to enable the Scottish Government to deliver support for the Highlands and Islands in a way that ensures neither the Highlands and Islands or Scotland’s public finances suffer as a result of this apparent defect in APD.
“I cannot see ADT put into operation with this significant uncertainty hanging over the Highlands and Islands.
"I therefore urge the UK Government to step up to the plate, to recognise their responsibilities and to support our proposal which would enable ADT to go forward as planned without causing harm to the Highlands and Islands economies.”
Scottish Conservative finance spokesman Murdo Fraser said: “The policy of reducing this tax has been a longstanding one, and eagerly awaited by the tourism industry.
“With the support of the Scottish Conservatives, there is a clear majority at Holyrood for making sure it happens.
“It’s therefore extremely disappointing to see the SNP trying to weasel out of this commitment, and many in the sector will feel badly let down.
“A cynic might conclude that today’s announcement has more to do with politics, and the SNP’s desire to cosy up to the Greens over the budget again, than legal technicalities.”
Scottish Greens finance spokesman Patrick Harvie said the news was "the latest nail in the coffin of a plan that has no social, economic or environmental credibility".
"Scottish Ministers might feel they need a technical excuse for dropping their plans this year, but the longer term issue remains that the SNP's policy on this is unjust and unsustainable.
"We cannot have cuts to aviation tax in the forthcoming Scottish budget or there's no possibility of Green MSPs and Scottish Ministers meeting to discuss a way forward.
Scottish Labour transport spokesman Neil Bibby said: “The SNP is using a convenient opportunity to kick a bad policy into the long grass.
“The SNP’s ADT cut is bad policy. Instead of delaying it, it should be cancelled. The SNP cannot justify a multi-million-pound tax cut for the frequent flying few at a time of real hardship and austerity for the people of this country.”
However, aviation industry leaders said the problem could be resolved.
Gordon Dewar, chief executive of Edinburgh Airport - Scotland's busiest - said: “We are naturally frustrated as this is a conversation we have been having for far too long without any meaningful outcome, and the tourism industry continues to miss out on the benefits of this cut.
"Our understanding of the issue is that the current exemption is unlikely to be challenged and even if it is, it’s likely to be found compatible with state aid rules."
Tim Alderslade, chief executive of Airlines UK, said: “We have been engaging with the Scottish Government and civil servants at Westminster about the situation with respect to the state aid exemption for HIAL airports and believe that a solution can be reached."