'Secret police recruit'
Garb, a South African Jew, said he was recruited by Shin Bet, Israel's secret police.
"To members of the public they [El Al employees] will represent themselves as airport security ... But in fact we were working for the Israeli security agency, which is the internal security service of the government of Israel," Garb said.
Watch the Carte Blanche report 'Take Off' with the 'confessions' of Jonathan Garb, above
"What we are trained [for] is to look for the immediate threat - the Muslim guy.
"You can think he is a suicide bomber, he is collecting information.
"The crazy thing is that we are profiling people racially, ethnically and even on religious grounds ... This is what we do."
Following up Garb's claims, the programme sent an investigator of Arab origin with a hidden camera to El Al's security area at the airport.
The report showed the man being stopped and questioned by a security guard.
When the reporter protested that he was not flying but waiting for a friend, a security manager from El Al arrived to further question him.
Carte Blanche's report revealed that former staff had accused El Al of smuggling weapons licensed to the local Israeli embassy, into the airport for use by the guards.
People guards deemed as suspicious could be held in a room out of public view, where they were interrogated and subjected to strip searches while their luggage was taken apart, the report showed.
Clandestine searches of their belongings and laptops are also carried out to identify useful documents and information, Garb said.
These actions violate South African law, which only authorises the police, armed forces or personnel hired by the transport ministry to carry out searches.
South Africa has threatened to deport all of El Al's security staff, while the Israeli foreign ministry has purportedly sent a team to South Africa to try to answer the South African government's concerns.
Yossi Levy, a spokesman for Israel's foreign ministry, said "the ministry cannot comment on security matters", but flights from South Africa to Israel were not at risk of being cancelled as a result of the diplomatic crisis, Ynet news reported.
Garb said: "This here is a secret service operating above the law in South Africa.
"We pull the wool over everyone's eyes. We do exactly what we want. The local authorities do not know what we are doing."