Chen already is in the center of a controversial campaign to gain full independence for Taiwan from China.
His latest order has angered nationalist politicians and may draw similar reaction from China, which opposes any attempt to separate the island from the mainland, reports The Times of London.
Chiang, who ruled Taiwan for 26 years after fleeing the mainland at the end of a civil war with the communists, had vowed to reclaim the mainland.
Under the new order, Taiwan's Defense Ministry plans to remove more than 100 fiberglass statues, saying they have been damaged.
John Chiang, the late general's only descendant still active in politics, says the effort is the latest in a series of steps by Chen to tarnish the image of the Nationalist Party.