The SNP faces a major struggle to get its budget through Holyrood this winter, after opponents reacted strongly against Alex Salmond's warning that he is legally entitled to ignore votes of the Scottish Parliament.

LibDems and Labour aim to change the rules by which the budget is decided, removing the current barrier to opposition MSPs putting down amendments as the legislation is scrutinised.

Tavish Scott, LibDem finance spokesman, was incensed at Mr Salmond for his warning that resolutions of Parliament can be ignored. But the First Minister was backed on Thursday by Presiding Officer Alex Fergusson.

He explained that the Executive must abide by laws passed by MSPs, and by votes of no confidence and on the Parliament's income tax-varying powers - but it is not required to act on other votes.

Mr Scott responded: "We've lived through so many sanctimonious lectures from the SNP in opposition, and now they're saying they're going to ignore the will of Parliament. It is very unwise of Alex Salmond to say what he said, and the equivalent of a declaration of warfare. They're in for a hell of a rough autumn."

The row was sparked by a difference in opinion over the proposed Edinburgh airport rail link and the capital's tram scheme. The SNP wants to scrap both to use the funds on other priorities, but the majority of MSPs want to retain them, as approved by the previous session of Parliament.

The combined £1.1bn budget is the first skirmish over money, as parties look ahead to the process of deciding how next year's budget of more than £30bn should be spent.

The decisions on spending powers for the year from next April should begin from this September, though the process will be stalled by at least a month because of a delay in the Treasury's announcement of the Scottish block grant.

Nevertheless, Mr Scott insists that ministers should make their plans clear within this month, and appear before committees for the maximum possible scrutiny.

The way the budget process was set up eight years ago is designed to help Executive ministers deliver their priorities, even if their MSP support is in a minority. The opposition can make recommendations about what should be in and out of the Budget in committee reports to Parliament, on condition that requirements to add spending in specific areas are equalled by cuts elsewhere. But the Executive is not bound to accept those suggestions.

Only one opposition MSP has tried to alter the Budget at the one stage when an amendment can be tabled. That was Nicola Sturgeon, when she tried to introduce payments to NHS patients who contracted Hepatitis C, but her tactic failed to win enough support.

Once the Budget Bill is in Parliament, only an Executive minister can propose an amendment. And if the opposition does not approve of the SNP's budget, the only way it can stop it is to vote it down. That would automatically revert to the budget allocations for the previous financial year.

Mr Scott wants the budget rules to change, so that the majority opposition can have clout in shaping it. A senior Labour source said the party is also aiming to change standing orders so that can be achieved. If the opposition combine their votes and secure that change, it would open the door to the opposition building up alliances to thwart SNP spending priorities.

The Labour source said: "We have one incredibly blunt instrument to accept or reject the Budget, and we would prefer subject committees to have the power to move amendments. We need a more flexible mechanism that actually works and lets the Parliament exert its will on financial matters, rather than having a nuclear button."

Derek Brownlee, the Tory finance spokesman, said of Mr Salmond's comments on the powers of Parliament: "Clearly, he's right in legal terms. But politically, it wasn't as deft as the other things he's been saying in Parliament."