The refugees were apparently killed, security sources said on Sunday, adding that eight others have been injured.
Ambulances were sent to the site of the assault south of the town of Rafah on the border between Egypt and the besieged Gaza Strip.
The Interior Ministry, which is in charge of the police, had no immediate comment on the incident.
No further details have been so far made available about the perpetrators of the attack.
The Israeli regime’s strict policy towards asylum seekers includes building a fence along the Egyptian border, denying illegal migrants work permits and holding them in a detention center in the desert.
A report by The Washington Post said in May that Israel has spent more than USD 350 million to build a fence along the entire border with Egypt to block the entry of Africans, mostly from Sudan and Eritrea.