Cairo security chief Gen. Ismail Shaer said 14 people were arrested and seven police were among the injured in the clashes with the largely Christian garbage collectors who raise pigs on the refuse and live in the teeming slums of Manishyet Nasr outside the capital.
Police were sent in after farmers resisted initial efforts by government workers to haul their pigs away.
Egypt last week ordered the slaughter of all the country's 300,000 pigs even though no cases of swine flu have been reported here. The World Health Organization has said the move was unnecessary because the virus is being spread through humans.
The campaign has been met from the start by protests and resistance from the impoverished farmers. The consumption and raising of pigs is largely restricted to the country's Christian minority, estimated at 10 percent of the population. Muslims consider pork unclean.
Authorities have now expanded the rationale for the slaughter beyond swine flu to a larger campaign against unsanitary pig farming conditions, particularly in the Cairo slums where the garbage collectors live.
In 2008, President Hosni Mubarak ordered all animal rearing, particularly pigs and chickens, to be moved out of populated areas for hygienic reasons. The order was never implemented, however, and authorities say the current crisis is a perfect opportunity.
Pig raising will be restarted in two years at specially constructed farms in the countryside using newly imported animals, officials from the Ministry of Agriculture told Egyptian media.
"Everything Egypt has decided to do - despite the noise it caused here and there - first and foremost aims at protecting human health, and the health of the Egyptian people which is worth all the efforts and the measures taken," presidential spokesman Suleiman Awwad said Sunday.
He added that the measures had the full support of the leaders of Egypt's Christian community.
Egypt was severely affected by the outbreak of bird flu in 2007 with more than two dozen fatalities in the past two years. Some 25 million birds were slaughtered and the rearing of poultry in households largely ended.
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