He’s talking about Communism, which is why he opens the speech by mentioning that Marx worked for a newspaper.

The point of the speech is to encourage newspapers to exercise restraint against publishing information which could impact national security.

https://www.jfklibrary.org/archives/other-resources/john-f-kennedy-speeches/american-newspaper-publishers-association-19610427

“ It is a system which has conscripted vast human and material resources into the building of a tightly knit, highly efficient machine that combines military, diplomatic, intelligence, economic, scientific and political operations.

Its preparations are concealed, not published. Its mistakes are buried, not headlined. Its dissenters are silenced, not praised. No expenditure is questioned, no rumor is printed, no secret is revealed. It conducts the Cold War, in short, with a war-time discipline no democracy would ever hope or wish to match.”

I don’t see the point of taking that little bit out of context. There’s no ambiguity what he’s talking about.