The sculpture of Themis - the goddess of justice - wearing a sari was less than six months old, but Islamist groups demanded its removal as they claimed it hurt the religious sentiments of Muslims.
Chief Justice Surendra Kumar Sinha ordered the removal of the sculpture from its existing location to be reinstalled in front of the Supreme Court museum on a different location inside the apex court, Attorney general Mahbubey Alam said.
The move prompted mass protests with demonstrators from the rights group Ganajagaran Mancha, mostly students, gathered in front of the court to protest against the removal.
Sculptor Mrinal Haque, who erected the statue, said that it is being removed to maintain peace.
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Haque, who along with four to five workers were overseeing the removal work said, "I don't know where the statue was kept though the authorities told me it might be reinstalled near the apex court's annex building", The Daily Star reported.
The statue was erected in December 2016, holding a sword and the scales of justice in her hands.
The statue, which is not of the Greek goddess but a Bengali woman, has ruffled feathers in the Muslim-majority nation, with hardliners staging massive protests in recent months.
According to the hardliners, the statue, a variation on the Greek goddess Themis, goes against Islam, the report said.
Witnesses said scores of slogan chanting protestors rallied near the apex court complex where police hurled tear gas canisters and coloured water from water cannons to disperse them.
In April, Prime Minister Sheikh Hasina, who leads the secular Awami League party, apparently backed the Islamists by expressing her dislike for the statue and approved its removal.
In reaction to criticism over her approval, Hasina said she had asked Chief Justice Surendra Kumar Sinha why the statue of a Greek goddess had been distorted by having it clad in a saree, the report said.
Bangladesh has experienced increasing tensions between hardliners and secularists in recent years, suffering a spate of killings of atheist bloggers, religious minorities and foreign.
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