Between 300 and 400 residents of the hilly Moqattam slum district of Cairo, where mostly Coptic Christian scrap merchants raise pigs, hurled stones and bottles at police.
Anti-riot police replied by firing rubber bullets and tear gas to disperse the demonstrators, most of them youths.
They want to steal our livelihood," protested one of the farmers, Adel Izhak, before police started to take control of the district.
Egypt's pigs mostly belong to and are eaten by members of Egypt's Coptic Christian minority and are reared by rubbish collectors in Cairo's shantytowns. Islam bans the consumption of pork for the majority Muslims.
Egyptian animal rights activist Amina Abaza deplored the slaughter of pigs and said the decision to cull them was probably taken only because they belong to the Copts.