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"During preparations for culling at one of the premises which is located in the protection zone, a notifiable disease could not be ruled out," a spokeswoman for the Department for Environment, Food and Rural Affairs (DEFRA) said.
The deadly H5N1 bird flu strain was confirmed at a farm in eastern England earlier this week. Suspicious deaths of turkeys at a nearby farm led to fears that virus may have spread, she said.
"All the poultry on the Suffolk premises are being culled under the slaughter-on-suspicion policy. At this stage we cannot confirm whether or not the disease is present," she added, noting samples had been taken and results were awaited.
Redgrave Poultry said the disease was originally confirmed at the Redgrave Park farm near Diss, Norfolk.
The company said on Thursday the second site was Grove Farm in Botesdale. Grove Farm shares the same workforce as Redgrave Park.
DEFRA said 5,500 free-range turkeys would be culled at the second farm.
The virulent H5N1 strain has killed more than 200 people worldwide since 2003 and millions of birds either have died from it or been killed to prevent its spread.
Britain's farm ministry has imposed a 3-kilometre protection zone, 10km surveillance zone and a wider restricted zone. In these areas, poultry must be isolated from wild birds and there are movement restrictions.
Britain had an outbreak of the H5N1 virus strain in February at a turkey farm in Suffolk, eastern England. © 2007 Australian Broadcasting Corporation