The set of 12 zodiac animal sculptures sit in the garden of the National Palace Museum's southern branch and are copies of high-profile ancient relics from China's Qing Dynasty.
They are seen on the mainland as emblematic of China's past suffering under foreign invaders. The originals of the statues were looted from Beijing's Old Summer Palace in 1860 by Anglo-French troops.
Hong Kong actor Chan is a member of the Chinese People's Political Consultative Conference (CPPCC) -- China's mainland's political advisory body -- and has drawn criticism in the past for his pro-Beijing remarks.
The attack came ahead of presidential elections in January, which saw Beijing-sceptic Tsai Ing-wen sweep to power, ending eight years of rapprochement with China under the previous Kuomintang government.
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Voters feared closer ties with Beijing threatened the island's sovereignty -- even though Taiwan is self-ruling, China sees it as part of its territory.
The museum said it planned to move the artwork after consulting with the public who expressed concerns over its political sensitivity as well as questioning its artistic value.
Lin said the museum would decide what to do with the removed statues after discussing the issue with the art industry later this month.
The two protesters who threw paint on the dragon and horse head sculptures in December were sentenced by a local court to two months jail earlier this year, according to local media.
They scrawled on the statues the words "cultural united front" -- a phrase used in Taiwan to refer to China's attempts to bring the island back into its fold through cultural influence.