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Among the hardest-hit stocks are such small-cap uranium miners as Denison Mines and Uranium Resources, which have fallen more than 50 percent this year.

Daniel Rohr, a senior securities analyst at Morningstar who covers the Canadian uranium miner Cameco, which has also fallen more than 50 percent, said he reduced his fair value estimate of the stock after Fukushima because of the potential political fallout.

“There’s more uncertainty about nuclear’s future, so investors need to be adequately compensated for the incremental risk they’re taking post-Fukushima,” Rohr told CNBC.com.

Investors felt the impact of the Japanese disaster immediately. Exelonand Entergy, U.S. utilities with the largest exposure to nuclear energy, fell 11 percent and 7 percent respectively in the week after the earthquake and tsunami, according to John Kohli, portfolio manager of the Franklin Utilities Fund.

While utilities in the U.S. have largely recovered since the earthquake, the pain for the industry isn’t over. The Market Vectors Uranium+Nuclear Energy exchange traded fund, which provides the broadest exposure among ETFs to the entire cycle of nuclear energy generation, continues to suffer. The ETF is down more than 28 percent through Oct. 21, compared with a nearly 9 percent drop in the Standard & Poor’s 500.

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