Mr Sillars, who was a vocal campaigner for the Yes camp during the 2014 referendum campaign, indicated he would abstain in a vote on self-determination for Scotland if it meant an independent Scotland would push to be readmitted to the EU.
He also warned First Minister Nicola Sturgeon that many who backed independence but voted Leave in the EU referendum would do the same.
Around 400,000 SNP supporters are believed to have voted to leave the EU, including a number of MSPs and former cabinet ministers, including former Health Secretary Alex Neil.
He accused Ms Sturgeon of behaving ‘hysterically’ for threatening to launch a second independence campaign if the UK government did not alter its course away from a ‘hard Brexit.’
Mr Sillars has been critically of the First Minister and the SNP for its pro-EU stance, having called for party members to back Brexit before the EU poll in June last year.
He also turned his back on his former party in the 2016 Holyrood election campaign, pledging his support instead to fledgling left-wing nationalist movement Rise over what he called the ‘soft selling’ of independence by the SNP for two decades.
His intervention will be a blow to the SNP leadership which is widely expected to announce plans for a second independence referendum at the party’s conference next week.