Japan's mapping agency is the latest in a series of government agencies to be targeted by hackers, raising fears that the breaches are part of a series of sustained attacks.
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Japanese officials say servers at the Geospatial Information Authority were breached in an attempt to access servers at a private cybersecurity company and a university.
The officials admitted that scientific data may have been compromised, according to the Telegraph.
Japanese officials are concerned that the latest attack shows hackers are attempting to take advantage of backdoor routes between trusted servers to access classified information.
The breach at the mapping agency follows reports last week of cyber attacks on computers in Japan's lower house of parliament, Japan's biggest defence contractor Mitsubishi Heavy, and nine of Japan's overseas diplomatic missions in the past few months.
The attack on Japan's lower house of parliament was reported to have been launched from a server based in China, but Chinese officials have denied involvement.
In June, internet giant Google said a cyber-spying campaign originating in China had targeted the Gmail accounts of senior US officials, military personnel, journalists and Chinese political activists.