Haganah were killing civilians too. These are the 3 massacres that involved 50+ civilians:
On December 31, 1947, the first large attack by the Haganah Zionist militia took place against the village of Balad al-Sheikh, east of the port city of Haifa, in which 60 to 70 Palestinians were killed, according to Walid Khalidi’s book, All That Remains.
Two massacres were carried out by the Haganah in Saasaa in 1948: One in mid-February and another at the end of October. According to Khalidi’s book, on February 15, a Palmach force raided the village of Saasaa and detonated explosives inside several homes, destroying 10 houses and killing “tens”, according to Haganah estimates. The New York Times reported at the time that 11 people were killed, five of them children, with 14 houses also destroyed.
The second massacre was perpetrated on October 30, when “mass murder” took place, according to Israel Galili, the former head of the Haganah National Staff. The exact numbers of those killed are unclear, nor are there detailed accounts of the killings, according to All That Remains. The village was eventually depopulated.
Before 1948, the village was known for being at an intersection that linked many urban centres, including Safad. It was dotted with water springs, apple and olive trees, as well as grape vines. In 1949, an Israeli settlement by the same name was established on the village site.
After this massacre, the Haganah was absorbed into the new IDF and massacres continued under the IDF name.