Labour leader Kezia Dugdale revealed the findings at First Ministers Questions today and said Ms Sturgeon's claim that education is her top priority is now "meaningless."
But the figures were rejected by the SNP leader who insisted that councils' own statistics suggest education spending has gone up.
The independent Scottish Parliament Information Centre (SPICe) report indicates that spending on every secondary school pupil has been cut by over £1,000 since 2011. In total, the figures indicate that £1.23billion has been taken out of schools, with spend per pupil across all stages down by £491 on average.
It comes as Scotland has fallen to all-time low in the international PISA education standings in key areas like reading, science and maths.
“Under the SNP, the official figures show that spending on pupils is going down again in real-terms, despite what John Swinney has claimed," Ms Dugdale said after First Ministers Questions.
“The SNP has cut spending by hundreds of pounds on every single pupil, and it’s cut spending on each secondary school pupil by over £1,000.
“It’s not the SNP reforms backed by the Tories that our schools need, it’s cold hard cash.
“Until Nicola Sturgeon commits to more funding for our schools, using the powers of this parliament, then her promise of education being her top priority is utterly meaningless.
“This week, teachers are going on their summer break. But what they really need is a break from this SNP government.”
But the First Minster told MSPs that data published on Tuesday which indicated that spending is on the up.
"Councils are planning to spend £144 million more - that's 3% in cash, 1.3% in real terms - on education this year, than they planned to spend last year.
"That includes the planned spend on the pupil equity fund of £120 million that I spoke about. Those, Presiding Officer are the facts.
"This Government is taking the tough action to reform out education system, to get more powers into the hands of headteachers and teachers and crucially, of course, to get more resources into the hands of headteachers and teachers."
She added that Labour councils in areas Like North Lanarkshire are axing support staff in schools and called on Ms Dugdale to "get her own house in order before criticising the Scottish Government."