The earliest I could find was a Jordanian reaction to the 1956 war, accusing Israel of inflicting "genocide" on Egypt.
The Soviet Union accused Israel of "genocide" for winning the Six Day War.
Yasir Arafat couldn't do any less. This is from 1968:
The irony, of course, is that very threat to attack Israeli civilians indeed would be a standard case of genocide under international law, since Fatah at the time was quite clear in its desire of "uprooting the Zionist existence."
In 1977, Moscow again accused Israel of "genocide" - because it was building houses in Judea and Samaria.
In 1982, Christians in Lebanon slaughtered hundreds of Palestinian Muslims. So, naturally, tthe Jewish state was accused of "genocide" (and a "holocaust," to boot.)
From the start, the slander was meant to tar Israel with the worst crime possible, the crime named after the Nazi extermination campaign against Jews. It was always a purely antisemitic slur, and it remains so today.
But notice how much the leftists of today are parroting the language used by the Soviet Union. Every baeless accusation against Israel - "apartheid" and "genocide" and "illegal occupation" - originated with the Soviet Union.