The birds have damaged properties by drilling holes into houses to store food and homeowners have been in a "long battle" with the birds, said Maureen O'Rourke, a spokeswoman for Rossmoor.
Audubon California, part of the National Audubon Society, issued a release Tuesday, expressing concern over the move to kill the birds.
"I know these residents feel they have tried everything to persuade the birds to not use residents' home, but they there are better options," Graham Chisholm, director of conservation for Audubon California, said in the statement.
Two of Rossmoor's 17 homeowner's associations obtained the permits to have the birds killed from the U.S. Department of Fish and Wildlife Service in June, according to O'Rourke.
Property that falls into the jurisdiction of the two homeowners associations includes some of the newest buildings in Rossmoor.
"They're in hilly open space areas," O'Rourke said.
She said homeowners spent years trying to rid of the birds before applying for the permits to have the birds killed.
"They've spent about $170,000 over the past eight years to fight them in other ways," O'Rourke said, adding that amount of money included repairs to buildings and bird proofing.
Some of the homeowners have tried using nets, Mylar, and fake owls and spiders to keep the birds away.
O'Rourke said personnel from U.S. Department of Agriculture is expected to come out to kill the birds within the next couple weeks.
Audubon California has offered assistance to the homeowners associations in considering other options and O'Rourke said representatives of the associations are expected to meet with Audubon staff.
Brian Murphy, a board member of the Mount Diablo Audubon Society, said members of the society are scheduled to meet with representatives of the homeowners associations Wednesday.
Murphy said the acorn woodpeckers are using the sides of homes as artificial granaries because old dead oak had been removed from the area during development.
He said by bringing in large pieces of dying oak and attaching them to trees in the area, the woodpeckers could make natural granaries, a possible permanent solution for keeping the woodpeckers from storing their food in homes.
Acorn woodpeckers are a relatively common bird in California that store food in large granaries drilled in oaks and other trees, according to Audubon California.