This question has been subject to debate before. As far as I know there has been no definitive answer.

One of the early scripts for the movie suggest the Rosatto Brothers were involved in Clemenza's death (possibly killing him by overdose of drugs).

My own 2¢ - Francis Ford Coppola purposely left vague how Clemenza died for "payback" to Richard Castellano (because he didn't come to terms to appear in Part II).

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