The Criminal Investigation Bureau said in a statement that it would also offer necessary assistance to the Democratic Progressive Party (DPP) to protect its information.
The DPP, which favours Taiwan's independence from China, said that in the past four months, it had traced more than a dozen cyber attacks every day to Chinese Internet Protocol (IP) addresses.
It said that hackers mainly targeted its presidential campaign planning as the party gears up for the January 2012 elections against the incumbent Ma Ying-jeou of the Beijing-friendly Kuomintang party.
Observers say China would prefer Ma to win instead of DPP chairwoman Tsai Ing-wen.
The accusation comes after the California-based computer security firm McAfee said last week that 72 targets across 14 countries were victims of a massive global cyber-spying campaign, with China seen as the likely culprit.
Chinese state media decried that allegation as "irresponsible".
Taiwan and China have spied on each other ever since they split in 1949 at the end of a civil war. Beijing still regards the island as part of its territory awaiting reunification, by force if necessary.
Taiwan's government websites have frequently faced cyber attacks, usually during disputes between the island and the mainland.