He was relieved from the post from Thursday.
Naidu, a staunch supporter of legislator Y Sampangi, had submitted his resignation after Sampangi had been disqualified from the Legislative Assembly.
The government had, however, not taken any decision on the resignation, which was submitted in November.
Reliable sources in the Urban Development Authority confirmed that the resignation was finally accepted on June 9.
Authority Commissioner Bheemanedi said that all facilities extended to Naidu were recalled on Thursday.
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