In 1853, President Franklin Pierce appointed Palmer Superintendent of Indian Affairs for the Oregon Territory. The debate of what to do with Native Americans ranged from full integration to total extermination. Palmer proved effective negotiating "Cessation of Hostility treaties" with the native tribes in 1854 and 1855, brokering nine of fifteen treaties. He joined Isaac Stevens, his counterpart for the Washington Territory, in the successful Walla Walla Treaty Council of the Yakima Indian War. Approximately 5,000 Indians attended deliberations from May 29, 1855 to June 11, 1855.