According to Volume XVIII of Japanese Diplomatic Documents, the official archives of Japan, Nishimura, the magistrate of Okinawa, submitted a report to the Japanese Ministry of Internal Affairs on September 22, 1885, following an investigation conducted under orders from the the ministry. Nishimura's report read: "With regard to the uninhabited islands located between our prefecture and Fuzhou of the Qing Dynasty, a secret investigation was conducted in accordance with orders received by Prefecture Secretary Morimoto from the capital. Please refer to the attached appendix for a summary of the investigation. Kume Aka-shima, Kobi and Chogyo have been place names in our prefecture since ancient times.... I dare not raise any objections with regard to the matter of the islands being under the jurisdiction of Okinawa-Ken However, the physical features of the islands are quite different from those of Daitojima which is located between our prefetune and Ogasahar Island. A report on the latter has been submitted under separate cover. I am convinced that they belong to the same islands and are located in the same area as the Diaoyutai, Huangweiyu and Chiweiyu islands recorded in The Record of Zhongshan. Obviously, Duke Zhongshan, whose title was conferred by the Qing government, got to know these islands when he undertook various voyages to the area, and named these islands as navigation marks in Ryukyu. Given these facts, I doubted the appropriateness of erecting markers on the islands during the course of investigation as we did on Daito-jima."

The secret investigation indicated that the Meiji government was already aware that the islands were not "unclaimed land", or at least they were areas that might create territorial disputes with China. However, then Minister of Internal Affairs Aritomo Yamagata expressed discontentment with the results of the investigation, and requested a second investigation in order to erect Japanese "territorial markers" on the islands. Although realizing that the islands were similar to those described in The Record of Zhongshan, Yamagata reasoned that the Qing government used them simply as navigation marks, and that "no other evidence or signs proving they belonged to the Qing state have been found". He also reasoned that different Japanese and Chinese names for the islands were insignificant, and further that the uninhabited islands were adjacent to the Yaeyama Archipelago.

Despite the fact that Japan seemingly agreed to put Yaeyama under China's jurisdiction in its plan to divide Ryukyu into two parts, it nonetheless harbored an ambition to "stretch an inch into a yard". It turned out, however, the results of the investigation prevented Yamagata from acting rashly.

On October 21, 1885, Japanese Foreign Minister Kaoru informed Aritomo Yamagata: "Based on a careful investigation and due consideration, we have determined that the islands in question are also close to the territory of the Qing state. When compared with our prior investigation of Daito-jima Island, we found that they cover smaller areas and that they have all been named by the Qing government. Qing newspapers recently published rumors that our government is attempting to seize the islands adjacent to Taiwan which are under Qing jurisdiction. They harbor suspicions of our country and repeatedly bring actions to the attention of the Qing government. Any attempt to openly erect state markers will definitely invite suspicion on the part of the Qing government. Therefore, we should limit our actions to on-the-spot investigations and drafting detailed reports on the configuration of various bays and on whether or not the islands have important resources which can be exploited in the future. Matters such as erecting territorial markers and undertaking development can be done in the future as the opportunity arises." Inoue also informed Yamagata that it would be totally inappropriate to make the secret Japanese investigation public via the media, and that the investigation should proceed in utmost secrecy in order to avoid opposition from China and the international community.

On November 24 that same year, Okinawan Magistrate Nishimura submitted the results of investigation to the minister of internal affairs and requested that the latter issue instructions in case disputes with China might arise. According to Nishimura, "As I noted in the previous report, the matter of erecting state markers will not necessarily be considered completely irrelevant to the Qing state. We may face trouble if conflicts arise." The very next day, Japan's ministers of internal and foreign affairs jointly issued the following order: "Ensure that no state markers are erected at the present time." Quite obviously, Japanese imperialists were at that very time accelerating arms expansion and war preparations, and awaiting the most opportune time to annex Korea and eventually engage in an all-out confrontation with the Qing government. It is equally as obvious they they did not want to act rashly to alert the enemy.