The confirmation of the democratic island's latest major data leak followed a report by local news channel TVBS on the hack of telecom giant Chunghwa Telecom.
That report included a screenshot of a post in which hackers announced they were "selling Chunghwa Telecom 1.7 TeraBytes of data" that included government contracts.
"The initial analysis of this case is that hackers obtained Chunghwa Telecom's sensitive information and sold it on the dark web, including documents from the armed forces, foreign affairs ministry, coast guard and other units," the defence ministry confirmed in a statement sent to AFP on Friday.
Taiwan is one of the world's top targets for cybersecurity attacks, according to digital data experts. Some have suggested that tactics employed against Taiwanese infrastructure bear the hallmarks of Chinese state-sponsored groups.
Beijing claims Taiwan as part of its territory and has never renounced the use of force to bring it under its control.
Taiwan's defence ministry added that an air force contract included in the Chunghwa leak was "not confidential information, thus (there was) no information leakage".
Correspondence between the navy department and Chunghwa also contained no classified information, the ministry said.
"We have asked the contractor involved to strengthen its information security control to prevent any further incidents," it said.
Neither the ministry statement nor the TVBS report identified the hackers or said where they were located.
Taiwan's Ministry of Foreign Affairs declined to comment on the leak.
Chunghwa, a publicly traded company, announced in a statement to the Taiwan stock exchange on Thursday that it had "conducted investigations to clarify the cause of the suspected incident".
"Currently, there is no significant impact on the Company's operations," it said, referring to potential losses from the data theft.
Government officials have said that persistent cyber threats are a form of "grey zone harassment" engaged in by China on a near-daily basis, including flying warplanes around the island and sending vessels to its surrounding waters.
While stopping short of clear acts of war, these tactics are enough to keep Taiwan's military and digital security agencies occupied, experts say.
Last year, Microsoft flagged the threat from a China-based group called Flax Typhoon that was targeting Taiwan.
The US tech giant said Flax Typhoon intended "to perform espionage and maintain access" to various Taiwanese organisations for as long as possible.
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