The massacre came after Chiang ordered his army to quell an uprising known as the 2/28 incident, sparked when an inspector beat a local female trader in Taipei for selling untaxed cigarettes.
Thousands of people were tortured and shot dead by Chiang's Kuomintang government during the subsequent crackdown, branded the "White Terror". The exact death toll is unknown, but some estimates put it as high as 30,000.
The bitterness has not subsided despite apologies by three presidents, including Ma, on behalf of the government since the 1990s.
On Saturday a fibreglass statue of Chiang in northern Keelung city was beheaded by unknown persons as the island commemorated the massacre. Several other smaller incidents of vandalism were also reported.
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The mayor of southern Tainan city said he plans to order the removal of all statues of Chiang in schools.
"Only with truth could there be forgiveness, and only forgiveness could there be reconciliation and peace," he said.
The 2/28 incident came two years before the Kuomintang fled the mainland, taking refuge in Taiwan after they were defeated by the Communist forces of Mao Zedong in a civil war.
The incident remained taboo for decades under Chiang's post-war rule, with the February 28 anniversary only officially marked after his death in 1975.
Anxiety has been growing on the island over ties with the mainland, which have improved markedly since Ma came to power in 2008. He was re-elected in 2012.
A proposed trade pact with the mainland sparked mass student-led protests and a three-week occupation of Taiwan's parliament last year.