Glen Innes Severn Council is under investigation by the Department of Primary Industries for allegedly dredging the Beardy waters without a proper permit.
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A DPI spokesperson confirmed the state government body "is currently investigating this matter".
"However, it would be inappropriate to discuss details of any investigations at this time," the spokesperson said.
"Feel free to check back at a later date."
Council General Manager Mark Riley said in a statement that council were informed they were under investigation on July 7.
"Council is cooperating with the Department in that investigation, and has every intention of continuing to do so," he said.
"Council has also sought legal advice in relation to matters raised by the Department."
He said he was unable to respond to a list of questions sent by the Examiner until that legal advice was finalised.
Council resolved unanimously to start dredging in March, ordering council officers to get approval to dredge, and then to begin extracting sediment "for use in topsoil products". At the time the estimate was that dredging would begin within weeks.
Director of Infrastructure Services Keith Appleby said at the council meeting on March 28 he had received first verbal and later written advice from a government department that dredging is legal, according to notes taken by the Examiner during that meeting.
A business paper distributed for that meeting mooted the idea of selling or using what is believed to be highly phosphorescent top soil in the sediment, which "poses a problem for water quality within the weir".
"It is envisaged that the mud could be blended with crusher dust to make an excellent product for Council and community use, and at the same time gradually improve the condition of the weir storage," says the Department of Infrastructure Services: Monthly Report report for February.
"It is recommended that Council extracts some material from the flats on a trial basis subject to obtaining any necessary approvals from the relevant NSW State Government agencies."
The weir is currently around 25 per cent full as of July 25, according to a council report published in the print version of the Examiner on Thursday.
Councilors were briefed about the investigation in the closed committee stage of the council meeting on July 25, resolving to keep informed of the situation.
Dredging of the weir has halted.