Mr Cadogan said the E. coli outbreak was one of the causes of a "significant public backlash that has come across my desk regarding freedom camping in the last few weeks''.
However, he said "that the outbreak is not caused by campers only resolves some of the concerns I have been hearing [about freedom camping] and does not mean that efforts to find workable solutions to other concerns will not be pursued by myself and council''.
Mr Sheppard said warning signs would remain in place until bacteria levels had reduced. Linz would also seek advice on whether anything could be done to manage the source of the contamination.
"Samples taken opposite the campsite and both up and downstream continue to show high levels of E. coli, so the warnings will continue to remain in place for now,'' Mr Sheppard said.
"Given that the test results confirm the contamination is not from the toilets or from other human sources, we will be looking to reopen the toilet block at Bendigo as soon as is reasonably practical. We will also keep the portable toilets brought in to help manage demand open as well, given that we still have high numbers of visitors.''