Local governments within 30 miles of nuclear power plants were required to develop the plans after an earthquake-tsunami catastrophe in March 2011, the Yomiuri Shimbun, which conducted the survey, reported Monday.
Japan's Nuclear Regulation Authority had instructed the prefectures and municipalities to complete the plans by Monday.
Officials of many local governments, particularly those with larger populations, said they faced difficulty in coordinating with some municipalities and securing suitable evacuation sites.
About 80 percent of the governments said they expected to be done with their plans by this fall.
The emergency plans must include provisions for medical care to treat victims of radiation exposure, a means of monitoring radiation, evacuation sites and methods of transporting evacuees to the sites.