The former Australia coach had missed the naming of his squad on Wednesday for internationals in November, including a Test against the world champion All Blacks in Tokyo on November 2, due to "illness" the Japan Rugby Football Union said.
The 53-year-old apparently complained of a severe headache on Tuesday and was taken to a hospital for tests, Kyodo news agency reported.
Japan general manager Kensuke Iwabuchi said Jones was conscious and able to talk, and that the Japan Rugby Football Union would wait until results of the tests were known before making any official decision or announcement.
Former South Africa coach Jake White, who co-opted Jones into his coaching setup during the Springboks successful 2007 World Cup campaign, said that he had been in touch with the Australian's wife.
"He is in intensive care and he currently doesn't have movement on his left side but he is talking and typical of Eddie it's about the challenge of the All Blacks and the subsequent European tour," White told South African rugby website keo.co.za.
"My understanding is he will be in intensive care for at least the next week."