Two investigations are currently looking into the social networking platform and whether it breaches competition laws, and the European Commission has demanded internal documents including 2,500 specific key phrases.
However, the company has claimed that would mean passing on unrelated and highly sensitive data.
Although the commission is set to defend its case in court - with the investigation ongoing - Facebook has filed an appeal to the EU courts against the breadth of the requests.
In a statement, the social media giant's competition lawyer Tim Lamb said: "We are cooperating with the commission and would expect to give them hundreds of thousands of documents.
"The exceptionally broad nature of the commission's requests means we would be required to turn over predominantly irrelevant documents that have nothing to do with the commission's investigations, including highly sensitive personal information such as employees' medical information, personal financial documents, and private information about family members of employees."
A Facebook spokesperson insisted the company isn't trying to hold up any investigation, and they stressed that the firm has been forthcoming with information thus far.
However, they noted that Brussels' request - which includes any documents featuring the phrases "shut down", "not good for us" and "big question" - could force the company to hand over confidential security assessments regarding its headquarters in California.