Professor Drew Scott, the partner of SNP MSP Aileen McLeod, has joined the government on a two-year secondment from Edinburgh University.
Already dubbed the government "Euro tsar", Scott is currently professor of European Union Studies at the university's School of Law.
Since January 3, he has worked three days a week advising ministers on EU treaties and "Scotland's European interaction" ahead of the referendum.
The Government will reimburse the university for Scott's time, meaning taxpayers pick up the bill.
The appointment is a tacit admission by ministers that they have been under-prepared on the subject. Labour said Scott's role showed ministers were "desperate" to end the blunders.
Deputy First Minister Nicola Sturgeon said Scott would be "invaluable" to ministers as they prepared to negotiate Scotland's entry to the EU in the event of a Yes vote in 2014.
Scott said he would help "deliver a European engagement strategy and provide expertise on EU institutions, treaties and policies" to help the Scottish Government define future options.