Israel deported to Egypt 91 illegal African migrants in four operations coordinated during the last two weeks of August, the State Attorney's Office said on 1 September.
A spokesman for the Israeli military, which patrols the state's borders, said it had returned them on government orders in line with the bilateral agreement signed with the Egyptian government.
However, rights groups are concerned that some were not given a chance to claim asylum in Israel.
Last year, Israel and Egypt agreed to clamp down on their porous border. "Israel cannot allow unfettered access to its sovereign territory," government spokesman Mark Regev told IRIN.
Several Israeli rights groups filed a petition last week in an attempt to halt the deportations. They said the Africans should be treated as asylum-seekers and be interviewed to make sure they were safe to return to Egypt.
Following the one previous use of the "hot return" policy - whereby Israel immediately returns captured infiltrators to Egypt upon arrest - rights groups had petitioned the court in August 2007 and received a response from the state saying it would not deport migrants without receiving assurances from Egypt regarding their welfare.
The UN Refugee Agency (UNHCR) in Tel Aviv said it was still awaiting clarifications from the Israeli government before "making a judgment" on the latest returnees.
"'The court must intervene immediately to stop the endangerment of lives of asylum-seekers," lawyers Anat Ben Dor and Yonatan Berman wrote in the urgent appeal filed on 27 August, which failed to prevent the deportations.
Brig-Gen Yoel Strick of the military's Southern Command said in his deposition to the court that there was what he termed a "specific failure"- meaning the "infiltrators" were indeed returned without a chance to present their cases for asylum, against Israeli official policy, but that there was no endemic problem.
To make sure the failure did not recur, the commander said soldiers would be briefed about questioning asylum-seekers but the immediate return policy would still be implemented.
Strick said he had received assurances from the Egyptians regarding the safety of the migrants.
The rights groups, led by the Hotline for Migrant Workers, said trained professionals and not soldiers should interview potential refugees and that the military was giving the job to inexperienced soldiers serving in mandatory draft or reserve services.
The NGO was also worried as the Egyptian government had sent migrants back to their country of origin, in some cases back to harsh conditions or internment.
News reports from Egypt suggested the Africans would be returned to their home countries and reported the migrants were Eritrean, Somali and Sudanese.
More than 8,000 mostly African migrants have crossed into Israel illegally in the past few years, rights groups and UN officials said.
Israeli officials have said an unchecked flow of migrants through the border posed economic and security risks for Israel.