It will then be mixed with lime and polymers to stabilise it before it is put back into the smaller pond, covered with green waste followed by a layer of clay, and capped off.
But Mr Hughes said the wild spring weather, which has brought rain and high winds, had affected the work which was now about a week behind schedule.
The sludge has been responsible for the foul odours coming from the wastewater treatment plant (WWTP) and which worsened from December last year. That prompted council to call in experts and ultimately deciding to spend $24 million upgrading the plant.
The first step means removing the sludge and contractors have been installing pipework around the lower settling pond diverting the city's waste directly from the upper main pond to ultraviolet light sanitisers before the waste is pumped into the sea.
The new plant, expected to be operating by early 2015, will see any sludge removed daily.
Residential and industrial waste will be pumped into a covered anaerobic pond, then shifted into stabilisation and clarifying ponds, before undergoing UV treatment and being pumped to sea through the South Beach outfall.
The council wants major work to start in March next year.