The SNP do not have a majority in Holyrood and need the support of at least two opposition MSPs to get their tax and spending plans through.
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The Greens have backed every SNP budget since 2016, but that now looks increasingly unlikely.
If the Finance Secretary fails to get her budget through it could ultimately lead to a snap election.
It seems unlikely that the Scottish Tories or Scottish Labour will support the SNP, though both parties insist they are engaging in good faith.
The Scottish Lib Dems have already made clear they will not back the budget if it contains any spending on independence.
Mr Greer said: “The Scottish Greens have always encouraged other parties to take budget negotiations seriously.
“The Lib Dems have at least entered the discussion this year and although their priorities are different to our own, we think this important debate is better off with a diverse range of proposals on the table.
“However, we would be deeply concerned if a pro-independence government axes entirely the already incredibly modest sum spent on independence preparations. If the SNP makes that choice, Green MSPs would find it impossible to support their Budget.”
“The SNP must categorically rule out this cut.” he added. “Conceding on this point would not only rule out the Scottish Greens’ voting for their budget proposals, it would destroy the wider independence movement’s trust in the Scottish Government.”
She added: “Any protection of or an increase in independence-related spending would sum up how disconnected Green and SNP politicians are from the public.”
A Scottish Government spokesman said: “Ministers are discussing the Budget with all parties and the draft Budget will be set out in the Scottish Parliament on 4 December.”
