The proposed plant is not in line with the county's 2004 comprehensive plan, said Alan Sobtzak, a commission member.
The application, which asks that the land be rezoned from agricultural to heavy industrial, will next be considered by county commissioners.
Don Gillispie, president of Alternate Energy Holdings, said in a statement that the company may start considering locations in Colorado or Mexico if the Idaho application is rejected.
He questioned why county officials recommended against rezoning the land.
"We find this puzzling as other forms of heavy industrial electrical generation, such as wind farms, solar plants and natural gas facilities, are given preferential treatment for siting under the county's comprehensive plan," Gillispie said. "These sources ironically consume much more ag land and/or are only niche energy, not to mention high-cost sources doing nothing for Idaho's base load power shortage needed to attract new businesses and much needed jobs."
The Snake River Alliance, a nuclear watchdog group based in Boise, praised the planning and zoning commission's decision.
"This is a huge victory for the people of Elmore County who spoke so eloquently and forcefully to defend Elmore County from this outlandish nuclear reactor scheme," said Andrea Shipley, the group's executive director. "We congratulate them for their passionate defense of their cherished way of life and the land and water that is so vital to these communities and to all of Idaho."