More than 60 German universities and academic institutions said in a joint statement that X was now incompatible with their principles.
"The platform's current direction is not compatible with the basic values of the institutions concerned -- openness to the world, scientific integrity, transparency and democratic discourse", they said.
Musk took over the platform, previously known as Twitter, in 2022 before firing about 80 percent of its staff, including those at content moderation teams.
Researchers say the site has turned into a haven for misinformation.
Musk defended the changes in a 2023 interview with Britain's public broadcaster, the BBC, saying they were necessary given Twitter's dire finances.
He has also described himself as a "free speech absolutist", with a permissive attitude towards content on X.
Musk also caused controversy in Germany on Thursday for broadcasting a discussion with Alice Weidel, leader of the extreme-right Alternative for Germany (AfD) party.
Parts of the party have attracted the attention of Germany's domestic intelligence agency for possible right-wing extremism.
The academic institutions which signed Friday's statement include Berlin's Humboldt University and a number of faculties which had already stopped using X, such as Berlin's Freie Universitaet.
"Changes on the X platform make it untenable to use it any further," they said, citing as an example the use of algorithms to boost "right-wing populist" content.
Two universities in the Austrian city of Innsbruck also put their names to the statement, which said the withdrawal from X "underlines the institutions' efforts for the sake of fact-based communication and against anti-democratic forces".
The universities are the latest in a string of German institutions to announce they are abandoning X.
On Thursday, the Federal Court of Justice said it would no longer post on the site, as did several labour unions.
In recent months, other businesses and organisations, such as Bundesliga football team St Pauli and supermarket giant Aldi Nord, have also quit X.
The German government said it has no immediate plans to stop using the platform.
Government spokeswoman Christiane Hoffmann told a press conference on Friday: "We are very concerned about how X has developed but at the same time we have to constantly weigh up how we can reach people whom we otherwise wouldn't be able to address."
"For the moment we have decided to keep using our channels on X but it is a constant process of evaluation," she said.
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