The reaction comes after Seoul's gender equality minister on Monday expressed support for efforts to include the papers.
The reaction comes after Seoul's gender equality minister on Monday expressed support for efforts to include the papers in the "Memory of the World" register of the United Nations Educational, Scientific and Cultural Organisation (UNESCO).
The plight of the women is a hugely emotional issue that has marred ties between the US allies for decades. Washington is keen for it not to hamper cooperation against North Korea's nuclear and missile programmes.
Mainstream historians say up to 200,000 women -- mostly from Korea but also other parts of Asia including China -- were forced to work at Japanese military brothels across the region during the conflict.
Japan, which ruled the Korean peninsula as a colony, was at war with China from 1937 and with the United States, Britain and other countries from 1941. The war ended with Japan's surrender in 1945.
Backing the registration of the documents "could go against the original mission and purpose of the establishment of UNESCO of fostering friendship and mutual understanding among member countries," Japanese foreign minister Fumio Kishida told reporters.
"We strongly conveyed our position to the South Korean government," he said.
Chief Cabinet Secretary Yoshihide Suga, the government's top spokesman, also said Japan "sent a strong message" to Seoul.
Chung Hyun-Back, the gender equality minister, hit back through her spokesman, saying the government will push through with the document registration as well as with a project she announced Monday to build a museum in memory of the women.
"The comfort women issue has become a global issue, not a bilateral one," the spokesman quoted Chung as saying. “We will be able to gather support from the international community."
In late 2015, under now-ousted president Park Geun-Hye, Seoul and Tokyo reached what they described as a "final and irreversible" agreement under which Japan offered an apology and a one-billion yen ($8.8 million) payment to South Korean survivors.
New President Moon Jae-In has told Japanese Prime Minister Shinzo Abe that most South Koreans cannot accept the agreement as it is, although he has not so far formally called for it to be renegotiated.
Suga, however, said Japan will not give up pushing Seoul on the issue.
"We will continue patiently asking South Korea to implement the agreement," he said.