Two police personnel were injured in the incident.
Manjhi had told reporters on Sunday that Brahmeshwar temple located at Andhrathadi village in Madhubani was washed after his visit during assembly by-poll campaign in July this year.
Bihar Director General of Police (DGP) P K Thakur today called it a "minor incident" and said the situation was under control.
The CM had said that Mines and Geology Minister Ramlashan Ram Raman and JD(U) MLC Vinod Kumar Singh had informed him about the purification of the temple, both of them have denied saying any such thing. Manjhi ordered a probe saying he had no confusion about the incident.
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The police said when the probe team of Kini and Ambedkar visited the village, the people insisted that no such incident had happened after the chief minister's visit. They also pointed out that temple is washed daily in the morning and evening.
They became angry when leaders belonging to two political parties also arrived to conduct their probe, said a police officer.
When the police personnel deployed around the temple for divisional commissioner and zonal IG's visit tried to control the crowd, they started to pelt stones on them.
In reply to another question regarding attack on Art, Culture and Youth Affairs Minister Vinay Bihari two days ago at a cultural programme in Rohtas district, the DGP said the DM and SP of the district were present at the event and a joint report has been called from them.