Sindh High Court Chief Justice Maqbool Baqar asked the provincial chief secretary, heritage secretary and advocate general to halt construction of the stage.
The order came in response to a petition that asked the court to take suo motu notice, stating that Mohenjodaro had been declared a heritage site by the UNESCO and the Sindh government should not use it for political purposes.
The petition stated that thousands of people would attend the opening ceremony of the Sindh Festival, which could put the ruins of one of the world's ancient civilisations at risk.
Bilawal, the son of slain former premier Benazir Bhutto, launched a campaign to conserve the heritage of his home province of Sindh with the two-week festival.
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The Mohenjodaro ruins built around 2600 BC are one of Pakistan's six UNESCO World Heritage sites that are deemed places of special cultural importance.
The ruins, discovered in 1922 by British archaeologist Sir John Marshall, are 425 km north of the port city of Karachi and are one of the largest settlements of the Indus Valley Civilisation.