The alert over the turkey farms in Valparaiso was raised on August 13 when the farm company said that egg production had dropped, the Chilean authorities said.
The properties have been quarantined and measures have been put in place to mimimise the health risk to consumers, they said.
"There is no evidence of the disease being present in the rest of the country," the Chilean agriculture ministry said.
But the infection is likely to heighten fears that a transmission of the flu virus to birds could lead to a possible mutation of A(H1N1).
World health authorities are concerned that swine flu could mutate with a strain of bird flu, creating a more deadly virus that is hard to treat.
At least 116 people in Chile have died of swine flu so far, figures released on Wednesday by Chile's health ministry said.
More than 70 per cent of the 1,800 deaths worldwide from the virus have occurred in South America.