An independent Scotland, with oil reserves, would become the third richest country in the EU in terms of GDP per head.
It is feared this would push up payments.
Figures in the Scottish Government's GERS (Government Expenditure and Revenues in Scotland) report estimated Scotland's share of the UK contribution to the EU at £124m.
That would rise to £378m if an independent Scotland managed to retain a share of the UK's existing budget rebate, worth £295m.
If ministers failed to negotiate a rebate, the bill would rise to £673m.
Many experts, including leading economist Professor John Kay, have warned an independent Scotland would have little chance of retaining a slice of the rebate.
However, Deputy First Minister Nicola Sturgeon insisted a deal to keep the discount could be struck.
It is said payments would rise as an independent Scotland, with oil reserves, would be among the wealthiest EU countries in terms of GDP per head. Only the Netherlands and Luxembourg would be better off.
Scottish Liberal Democrat leader Willie Rennie MSP said: "The SNP government's own figures have laid bare the real cost of the nationalist's independence plans. Even with the rebate an independent Scotland's payment to the EU would triple to £378m."
A Scottish Government spokeswoman said: "The EU Budget for 2014-2020 was agreed by EU finance ministers (subject to European Parliament approval). Up to independence Scotland will contribute to that as part of the UK and would then negotiate with the UK an appropriate division. In 2020 all aspects will be subject to fresh negotiations."