The presentation by Alessandro Strumia of Pisa University was delivered Friday at the Geneva lab during a workshop on the relationship between high energy theory and gender.
The presentation -- which includes various slides, charts and graphs -- appears to suggest that men face discrimination in the field of physics.
One pictorial series suggests that women line up to take gender studies and then later protest over a lack of jobs in stem fields, an umbrella term that covers areas like chemistry and engineering.
"Physics invented and built by men, it's not by invitation," one slide says.
"CERN considers the presentation delivered by an invited scientist during a workshop on High Energy Theory and Gender as highly offensive," the lab said in a statement.
"It has therefore decided to remove the slides from the online repository, in line with a Code of Conduct that does not tolerate personal attacks and insults."
CERN, the French acronym for the European Centre for Nuclear Research, is for the first time being led by a female director general: Fabiola Gianotti, an Italian expert in experimental particle physics, took charge in 2016.
The lab has said that despite efforts to close its own gender gap females still account for less than 20 percent of staff.
The lab notes that it has backed initiatives aimed at boosting female participation in the sciences.
"Diversity is a strong reality at CERN, and is also one of the core values underpinning our Code of Conduct," the statement said.
"The Organisation is fully committed to promoting diversity and equality at all levels."