China claims the self-ruled island as part of its territory and relations between the two have plummeted in recent years as Beijing has increased its rhetoric about "unification" being "inevitable".
Taiwanese authorities also say its government agencies face an estimated five million cyberattacks a day, which tech giants such as Microsoft have identified as tactics deployed by Chinese state-sponsored groups.
Taiwan Defence Minister Wellington Koo said on Tuesday an accusation from China that a shadowy group from the island was conducting cyberattacks against Beijing "is not true".
"China is the number one country conducting daily cyberattacks against Taiwan, and countries that share similar values," Koo told reporters outside parliament.
"The real initiator is China."
Koo's comments were in response to accusations by China's national security ministry on Monday that blamed a group it identified as "Anonymous 64" for "attempting to gain control of relevant web portals, outdoor electronic screens, network television".
The ministry also accused the group of broadcasting "content that denigrates" China.
It claimed that Anonymous 64 belonged to a cyber unit in Taiwan's defence ministry and identified three Taiwanese people it said were involved, urging the public to report "sabotage activities" to national security authorities.
AFP was not able to verify where the hacking group is based or whether it had actually carried out the cyberattacks Beijing alleged.
Koo said Taiwan's military is "protecting its people and defending our free and democratic life".
"China's statement will not have a chilling effect," he said.
The island defence ministry's Information, Communications and Electronic Force command has also denied China's accusations.
"The current hostile situation and cyber threats are severe," it said on Monday.
It also said in a statement Chinese forces "continue to disrupt Taiwan by means of aircraft, ship and cyberattacks, which are the cause of the disruption of regional peace".
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