Habtom Zarhum, 29, was shot by a security guard at a bus station in the southern city of Beersheba Monday after being mistaken for an assailant in an attack that killed an Israeli soldier.
Footage of him bleeding as an angry mob rained blows on his head and body has spread rapidly on social media, prompting soul searching among Israelis over their response to a wave of attacks as well as their treatment of African migrants.
Public radio said two of them work for the prisons system.
The police statement said the four would go before a judge Thursday.
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Zarhum's autopsy ruled he died of gunshot wounds, rather than the vicious beating he received from bystanders as police officers looked on.
His death comes in the middle of a surge of violent attacks across Israel and the occupied West Bank that has seen at least 47 Palestinians killed, often after knife attacks targeting Jews.
Following Zarhum's death, Netanyahu publicly called on Israelis not to take justice into their own hands, but many see the young man's killing as part of a wider problem in Israel's treatment of African asylum-seekers.
Official figures show 45,000 illegal immigrants are in Israel, almost all from Eritrea and Sudan. African communities complain of marginalisation, and they have held several protests this year against their alleged mistreatment.
The UN says as many as 53,000 refugees have crossed Israel's southern border with Egypt, including 36,000 from Eritrea.