The SFC said the shortfall was driven by an under estimate of the number of additional and higher rate income taxpayers north of the border.
The figures published in a SFC evaluation report will not have an impact on the Scottish budget because shortfalls are cushioned by an adjustment to the block grant Scotland receives from the Treasury.
In May, SFC estimated income tax liabilities of £11.3 billion for 2016/17.
However, final outturn figures published by HMRC show receipts were actually £10.7 billion, a difference of £550 million or five per cent.
The forecasts were made using data from the 2015/16 Public Use Tape (PUT), a publicly available anonymised version of the Survey of Personal Incomes (SPI), a sample of HMRC taxpayer records.
SFC said the data was “the best available source of information on income tax liabilities for Scotland” at the time.
Its report added: “We believe most of this headline error of £550 million is because of data issues.
“Differences in the estimated number of taxpayers with higher levels of income between the PUT and outturn data appears to contribute a significant amount to the total error, in particular differences in the number of additional rate taxpayers.”
Shadow finance secretary Murdo Fraser said: “This analysis shows there are considerably fewer earners on higher and additional rates than the SNP government thought when it was plotting its tax hike.
“That means future tax receipts could be badly out, and that will have an impact on the Scottish Government’s ability to pay for hospitals schools and infrastructure.
“It also proves the need for a rethink on taxation.
“We need to be encouraging higher earners to come to Scotland, not driving them away with rates higher than anywhere else in the UK.”
He added: “As these figures show, a smaller number of higher rate taxpayers translates into a significantly lower tax take – and that can have serious financial consequences.”