A vacation bench comprising justice Rajan Roy and justice S N Agnihotri quashed the order on the grounds that they were not provided an opportunity of hearing, which was mandatory under the Waqf Act 1995.
The court, however, gave liberty to the state government to proceed afresh in accordance with law.
The Uttar Pradesh government had passed the order on June 16, saying these members had allegedly indulged in irregularities in connection with waqf properties.
The members who were removed included Akhtar Hasan Rizvi, Syed Wali Haider, Ashfa Zaidi, Maulana Azim Husain Zaidi, Aalima Zaidi and Najmul Hasan Rizvi.
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All these were nominated by the previous Samajwadi Party government.
On June 15, the Uttar Pradesh government, after ordering dissolution of Shia and Sunni waqf boards, had also recommended a CBI probe into the alleged irregularities worth crores of rupees committed by the two bodies in the state.
There have been serious allegations of corruption against the Shia and Sunni waqf boards related to their properties.
The role of the chairman of the Shia Waqf Board Wasim Rizvi as well as the minister for waqf in the previous Samajwadi Party government Azam Khan had come under the scanner after the inquiry by the Waqf Council of India.