"The authorities took advantage of the situation to resolve the question of disorderly pig rearing in Egypt," health ministry spokesman Abdelrahman Shahine told Agence France-Presse (AFP).
The World Health Organization's move to put the pandemic alert to phase 5 confirms that the situation is not a pig problem but a human problem, he added. The government is calling the decision a "general health measure" rather than a measure to fight swine flu.
So far no cases of the new virus, which has hit 11 other countries, have been reported in Egypt. However, Egypt does have experience of avian flu, a much deadlier strain that has killed 22 people in Egypt between 2004 and 2008.
The World Organization for Animal Health OIE said it was "inappropriate" to cull pigs as a precaution against the new flu virus and countries should instead focus their efforts on increasing surveillance and strengthening biosecurity.
"The OIE advises members that the culling of pigs will not help to guard against public or animal health risks presented by this novel A/H1N1 influenza virus and such action is inappropriate," said the OIE in a statement reported by Reuters.
The United Nations' Food and Agriculture Organization (FAO) agrees. Both organizations are urging countries to stop using the term "swine flu" to describe the new virus.
The vast majority of Egyptians are Muslims and don't eat pork for religious reasons. However, about 10 per cent of Egyptians are Coptic Christians, and so are most of the pig farmers, many of whom live in Cairo slums inhabited mostly by Christian garbage collectors. The pigs feed on the garbage.
The Egyptian agriculture ministry's head of infectious diseases, Saber Abdel Aziz Galal told AFP that the government wants to restructure pig farming so that it takes place on "good farms, not on rubbish". At the moment the pigs live with "dogs, cats, rats, poultry and humans, all in the same area with rubbish," he said, explaining that the goverment wants to build new farms in special areas, like they have in Europe.
"Within two years the pigs will return, but we need first to build new farms," he said.
The move has angered many of the pig farmers, and several of them in Cairo told the press that this latest move was yet another example of resentment against Christians by Egypt's Muslims. According to the New York Times, last year there were several violent incidents, including the kidnapping and beating of monks.
There was at least one violent clash on Thursday when farmers threw stones at veterinary agents who came to collect some pigs.
While some slaughtering started on Thursday, Agriculture Minister Amin Abaza said that the mass cull would begin in earnest on Saturday.
According to AFP, the middle east news agency MENA reported that Abaza said it will take about a month to kill all the pigs. The culling will take place in special slaughterhouses that have been checked for swine flu, he added.
The health ministry will also start monitoring the health of 34,000 rubbish collectors, particularly those working near pig farms, said the MENA report.
A New York Times report describes the day to day life of one of the pig farmers, 26-year-old Barsoum Girgis who lives in a poor neighbourhood outside Cairo. Girgis lives on the first two floors of a building, with his extended family of 30 people. He has 60 pigs on the ground floor.
Girgis has two professions: garbage collection and pig farming. This is not unusual in a city where poor farmers rely on garbage to feed their stock. Girgis gets up at 4 am, goes to the city to collect garbage, gets back about 9 am, and sorts the garbage into what he can feed his pigs and what he can sell as scrap.
Girgis told the New York Times that he was worried about how he was going to feed his family and send his children to school if the government took away his livelihood.
It is not clear if the government will be compensating the pig farmers. Galal told AFP that at first they would just be getting the animals back as meat and there would be talks about compensation later.
Other media have mentioned amounts in the region of 1,000 Egyptian pounds, (about 180 US dollars) per farmer.
In the meantime armed police are stationed outside some of Cairo's pig farming areas, to stop pig farmers trying to smuggle out and hide their pigs, as one farmer with 300 pigs tried to do on Wednesday.
Egypt reported 22 deaths during the bird flu outbreaks between 2004 and 2008, and although the new flu is not the deadly H5N1 strain, but a variation of the H1N1 strain that causes seasonal flu in humans every year, it does contain genetic material from human, bird and pig flu viruses, and thus must have circulated in pigs at some stage in its history.
Pigs are a well known source of health risks for humans, and while in this case it appears that the risk of becoming infected with the new strain of "swine flu" is not linked to pigs, there is evidence that some diseases are, and this may well be one of the reasons behind the Egyptian government's decision to reorganize the country's pig industry.
For example, a study published in the June 2008 issue of Clinical Microbiology and Infection, noted that screening of Dutch pig farmers and pigs found that over 20 per cent of the farmers and nearly 40 per cent of slaughterhouse pigs tested positive for an unusual strain of MRSA (methicillin-resistant Staphylococcus aureus) belonging to a sequence type that has caused human infections in several European countries, Canada and Singapore.
The study concluded that:
"A concerted effort on the part of clinicians, infection control practitioners and veterinarians will be required to prevent further spread of this novel strain of MRSA."
Main sources: AFP, New York Times, Reuters.