The report said the technology was collecting information about what pupils and teachers did on their sites, and sent that data back to Facebook.
That data could then be used by EdTech websites to target advertising on Facebook and Instagram.
"Facebook can also retain and use this data for its own advertising purposes, although it is not always clear what these purposes are," the report said.
Facebook Pixel was also used to collect personal data and create shadow profiles for people who had never used their services or signed up for an account, it said.
An Education Perfect spokesman said it had always taken the topic "very seriously".
The company continuously invested in information security and data privacy infrastructure and controls as well as being periodically audited by independent third parties, government agencies and school groups.
Education Perfect had written to Human Rights Watch confirming its allegations regarding the use of pupil data were "factually inaccurate".
It did not track or share data with third parties or use keystroke-logging software to monitor pupils' work and send gathered data to third party companies.
"Any reference or statement that we are using trackers in the EP learning platform is factually incorrect," the spokesman said.
It would be engaging with an external auditing firm to verify its position to provide "peace of mind" to schools and pupils.
Education Perfect would also be creating a set of webinars to provide transparency in its approach, the spokesman said.
Last year, global investment firm Kohlberg Kravis Roberts (KKR) bought a majority stake in Education Perfect in a deal valuing the company at $455 million.
The company now has offices in Australia, New Zealand, Singapore and Dubai, and is being used by more than a million pupils and 50,000 teachers in 3000 schools across 50 countries.
The Otago Daily Times put several questions to KKR yesterday about whether it was comfortable with what had been alleged. It declined to comment, referring the ODT back to Education Perfect.
-- riley.kennedy@odt.co.nz