Some of the affected websites appear to not have patched a code execution vulnerability nicknamed the Shoplift Bug Patch, Magento's security team wrote in a blog post. A patch was released in February.
Other Magento-powered sites have not applied other patches, making them vulnerable.
The latest attack against Magento was highlighted by Malwarebytes and Sucuri, two security companies, who noticed attacks on the client and server sides.
The infected Magento sites contained malicious scripts that created iframes, which pulled content from the malicious domain "Guruincsite." That domain, which is blacklisted by Google, has been linked with the Neutrino exploit kit.
If encountered by someone browsing a website, exploit kits attack a computer, looking for software vulnerabilities in order to deliver malware. Hackers often try to plant code that triggers exposure to an exploit kit on legitimate, highly trafficked websites, as it creates an opportunity to infect many computers.
Malwarebytes saw client-side exploits coming from Neutrino that try to exploit Adobe Systems' Flash Player and installs malware called Andromeda/Gamarue, wrote Jerome Segura, a senior security researcher, on Sunday.
"Compromised machines can be harvested for financial credentials and also become part of a large botnet," he wrote.
Magento warned that even if all patches have been applied to the software, it's important to figure out if a website had been compromised prior to patching.
Even if a flaw has now been patched, it's possible the attackers created unauthorized administrative accounts, which would continue to give them access, Magento said.
Magento, which is owned by eBay, is an attractive target for attackers since it's used by a large number of companies, including Nike, Olympus and Ghirardelli Chocolate. It claims to be the most used software for the top 1 million websites ranked by Alexa.