No obvious military activity can be seen in the clip, which appears to show the docked Izumo helicopter destroyer.
According to officials, footage "purportedly shot by a drone" was first uploaded to Chinese video-sharing platform Bilibili on March 26.
It has since been viewed around 187,000 times on the platform, and has also proliferated on Douyin, China's version of TikTok, and on a Chinese-language X account.
"It is likely that footage in question was actually shot," a Japanese defence ministry official told reporters on Thursday, after an analysis.
Flying drones over military facilities in Japan is illegal.
"Should a drone be used to attack our defence facilities, it could cause significant disruption to our security and defence," the official added.
"From this standpoint, we take the outcome of our analysis very seriously."
The ministry declined to comment on whether it had detected the drone's intrusion, citing security concerns.
The official said the ministry will seek to prevent a recurrence by using electronic jamming and operating anti-drone devices with higher capabilities.
In April, Defence Minister Minoru Kihara said that he was aware of the footage circulating on Bilibili, and the ministry was probing the possibility it might have been "doctored or fabricated with malicious intent".
They remained mum however on who the perpetrator may have been or the possible motive, including whether there were any links to China.
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