The sculpture of Themis - the goddess of justice - wearing a sari was less than six months old, but Islamist groups demanded its removal by Friday.
They claimed it hurt the religious sentiments of Muslims and it prompted mass protests in the capital Dhaka.
PM Sheikh Hasina agreed to its removal, but secular groups opposed it.
Workers came with equipment and a crane at midnight to uproot the controversial statue, the BBC's Bangla service reported.
The statue is being removed to maintain peace, said its creator Mrinal Haque.
