The clip posted by independent newspaper Al-Masri Al-Yom includes gory images of pigs being beaten with iron bars, piglets being stabbed and animals being kicked alive into bulldozer buckets.
Although no case of A(H1N1) swine flu has yet been detected on its territory, Egypt is the only country in the world to have decided to kill all its pigs, estimated to have numbered around 250,000 before the cull began.
The World Health Organisation has said the drastic measure is not scientifically justified.
In the video, Mohamed el-Mugharbil, deputy mayor of Kashkus near Cairo, describes how chemicals are also poured on animals caged in lorries, leading to a slow death.
Ali Shaaban, head of the site where the corpses are buried, confirms the method. "The pigs are covered with chemical products and left for 30 or 40 minutes until they are dead, then we throw them in the ditch."
The agriculture ministry denied the animals are killed with chemicals. "These are disinfectants. The throats of the animals are slit before they are buried," Saber Abdel Aziz Galal, head of the department of infectious diseases, told AFP.
Other pictures obtained by AFP show pigs which have been disembowelled but whose throats have not been slit.
"Only the males are killed in accordance with the rules," said journalist Heba Nasreddin, while "the piglets and sows are hit with an iron bar and left to bleed to death."
An online petition calling on the Egyptian government to end the "senseless slaughter" has been launched on http://www.care2.com.
The slaughter caused controversy from its start on May 3, when riot police clashed with stone-throwing pig farmers trying to prevent their animals from being taken away.
The authorities have said it will take six months to complete the slaughter and announced plans to import three machines to boost culling capacity to 3,000 animals a day.
Arab intellectuals, both Christian and Muslim, have accused President Hosni Mubarak's government of having conspired with the Islamist opposition the Muslim Brotherhood, which opposes rearing pigs "on Islamic land."
"The Copts are victims of the flu without ever having been contaminated," according to Moroccan writer Tahar Ben Jelloun, who believes the government "clearly acted under pressure from Islamists" when it ordered the mass cull.
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