According to the Dawn news report, the incident took place on Wednesday in Bhong town, about 60 km from Rahim Yar Khan city.
Besides the vandalisation, the mob also blocked the Sukkur-Multan Motorway (M-5), the report added.
Citing sources, Dawn news said that a case was registered against the minor on July 24 based on a complaint filed by a cleric, Hafiz Muhammad Ibrahim, of the Darul Uloom Arabia Taleemul Quran.
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The sources said that "some Hindu elders did tender an apology to the seminary administration saying the accused was a minor and mentally challenged".
But, when a lower court granted him bail a few days ago, some people incited the public in the town on Wednesday and got all shops there closed in protest, the report quoted the sources as further saying.
A video clip showing people wielding clubs and rods storming the temple and smashing its glass doors, windows, lights and damaging the ceiling fans went viral on the social media.
In response, one Twitter user said: "Ganesh Temple, village Bhong in Rahim Yar Khan, Punjab has been ravaged. Another day, another attack on Hindus in Pakistan."
Another said: "Yesterday, mob ran amok at Temple over minor boy issue who allegedly urinated, boy said to be mentally handicapped. Hindu community made apology for boy — case registered against nine-year-old boy. Those vandalised temple, no FIR registered against them."
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District police spokesman Ahmed Nawaz Cheema said Rangers had been deployed in the troubled area and the situation was under control.
A small town close to the River Indus and Sindh-Punjab border, Bhong houses a number of gold traders who originally hail from Ghotki and Dehrki (Sindh), according to the Dawn news report.
A ruling PTI member representing minoritie said he had been in touch with the local Hindu community and influential Rais family of Bhong since the issue surfaced.