The two hospitals had treated Litvinenko before he died on November 23. His body was found to contain a large quantity of a highly radioactive material, polonium-210.
A spokesman for the agency, Lawrence Knight, said that both hospitals had been checked for radiation and found safe. He said all areas were open to the public.
According to the Health Protection Agency, more than 1,100 people called a special hotline after Litvinenko's death to express concerns they may have been contaminated. Sixty-eight of them, including the 49 hospital staff, were referred to health authorities.