Figures from watchdog the Electoral Commission showed the Nationalists spent just £90,830 on fighting to keep the UK in the bloc despite an upper limit of £700,000.
The party has seen a surge in donations and membership in recent years.
Critics said the spending showed the SNP gave June’s poll a “low priority” despite Nicola Sturgeon’s warnings cutting ties with Brussels could trigger another independence referendum.
It came as the First Minister concluded her two-day visit to Dublin by insisting breaking-up Britain remained “firmly on the table” in a speech to the upper house of the Irish parliament.
She received a warm response from mainly nationalist senators with several later defying convention to speak out in favour of a UK split during a question and answer session.
The SNP’s referendum spending was less than the £98,597 they laid out in unsuccessfully battling the Glenrothes by-election for Westminster in 2008.
Pub chain JD Wetherspoon, whose boss Tim Martin is an ardent Brexit supporter, spent £94,585 spent backing Leave.
Officials defended their spending highlighting Scots voted by a margin of 62 per cent to 38 per cent to Remain.
But the Leave campaign still managed secure more than a million votes north of the Border.
Scottish Tory MSP Murdo Fraser suggested the disclosure that former Cabinet minister Alex Neil and several other senior SNP politicians voted Leave may explain why so little cash was spent.
He added: “The SNP is behaving like leaving the EU is the end of the world for Scotland.
“But the party’s pitiful investment in the campaign tells another story completely.
“The SNP is not a poor organisation, yet it treated the EU referendum like it was a council by-election.”
Labour’s Europe spokesman Lewis Macdonald added: “The Nationalists barely lifted a finger during the EU referendum but now want to take advantage of Brexit by forcing another independence referendum on the people of Scotland. This would be an act of economic vandalism.”
The Electoral Commission statistics covered campaigners who spent less than £250,000.
Figures for those who spent more, including Labour, the Tories and official campaigns, will be published at a later date.
They showed the SNP spent £64,105 on leaflets and £26,725 on advertising. In contrast, the party spent £1.3 million in the 2014 independence referendum campaign.
Trade unions Unite, the GMB, and the shop workers’ union USDAW were among those who spent more than SNP in backing Remain.
Comedian Eddie Izzard also spent more than £36,000 campaigning to stay tied to Brussels.
Bill Kidd, an SNP MSP said: “This is a bizarre, boomerang attack which threatens to be a huge embarrassment for the Lib Dems, Labour and the Tories.
“The SNP ran a strong, positive and effective campaign, helping to successfully secure the overwhelming 62 per cent vote for Remain in Scotland.
“And given the attack they have mounted against the SNP, they must now publish figures showing exactly much they spent on the campaign in Scotland – and the verified accounts providing evidence of it.”
Addressing the Irish Senate Ms Sturgeon claimed it was clear that Brexit posed the “greatest foreign policy challenge that Ireland has faced since it joined the European Union.”
Ms Sturgeon confirmed proposals for Scotland to stay in the EU single market even if the UK comes out would be published by the end of the year.
She added: “Of course, there is also the option of considering again the question of becoming an independent country.
“And that option of course remains firmly on the table. If the path that the UK takes turns out to be deeply damaging to Scotland’s best interests, to our economic, social, and cultural interests, then the people of Scotland must have the right to choose a different future.”