Use the magento soap/rest api for creating a custom attribute for Product and update with values as well,
$proxy = new SoapClient('http://magentohost/api/soap/?wsdl');
$sessionId = $proxy->login('apiUser', 'apiKey');
echo "<pre>";
// Create new attribute
$attributeToCreate = array(
"attribute_code" => "new_attribute",
"scope" => "store",
"frontend_input" => "select",
"is_unique" => 0,
"is_required" => 0,
"is_configurable" => 0,
"is_searchable" => 0,
"is_visible_in_advanced_search" => 0,
"used_in_product_listing" => 0,
"additional_fields" => array(
"is_filterable" => 1,
"is_filterable_in_search" => 1,
"position" => 1,
"used_for_sort_by" => 1
),
"frontend_label" => array(
array( "store_id" => 0,"label" => "A new attribute" )
)
);
$attributeId = $proxy->call($sessionId,"product_attribute.create",
array(
$attributeToCreate
)
);
// Update attribute
$attributeToUpdate = array(
"scope" => "global",
"is_unique" => 1,
"is_required" => 1,
"is_configurable" => 1,
"is_searchable" => 1,
"is_visible_in_advanced_search" => 0,
"used_in_product_listing" => 0,
"additional_fields" => array(
"is_filterable" => 01,
"is_filterable_in_search" => 0,
"position" => 2,
"used_for_sort_by" => 0
),
"frontend_label" => array(
array(
"store_id" => 0,
"label" => "A Test Attribute"
)
)
);
$proxy->call(
$sessionId,
"product_attribute.update",
array(
"new_attribute",
$attributeToUpdate
)
);
I hope this will solve your problem..