China consistently reminds its people of the 1937 Nanjing Massacre in which it says Japanese troops killed 300,000 people in the then-national capital.
A post-war Allied tribunal put the death toll at 142,000, but some conservative Japanese politicians and scholars deny a massacre took place.
JOC Executive Board member Yosuke Fujiwara told Japan's Kyodo news agency that they were taking precautions to ensure their athletes were safe in Nanjing.
"When they are outside, we want them to be aware that it might not be totally safe," Fujiwara said.
"In the Athletes' Village we want them to wear the official Japan tracksuit, but in the city normal clothes are fine."
Deteriorating relations between Beijing and Tokyo have been fuelled by a row over a chain of disputed islands in the East China Sea. Ships from both countries frequently shadow each other around the islets, raising fears of a clash.
Ties have further worsened since China's creation of an air defence identification zone over the East China Sea and Japanese Prime Minister Shinzo Abe's visit to the controversial Yasukuni Shrine honouring war criminals among Japan's war dead.
The Second Summer Youth Olympic Games take place in Nanjing from Aug. 16-28.
(Writing by Peter Rutherford; Editing by John O'Brien)
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