The two men, part of the council's direct services department, were carrying out work on behalf of Welsh Water. It is believed both collapsed and died after being overcome by fumes.
Will Watson, director of the Neath Port Talbot DSO, immediately questioned why the men were found in the sewage chamber.
'There was no obvious reason for the men to have been in the chamber. When the operation commenced it was not part of the plan for the men to enter it,' he said.
More than 30 other people were treated for exposure to the chemicals before the chamber could be completely drained. Four local companies have been asked by south Wales police to stop discharging waste until the source of the two pollutants has been traced.
The two dead men were named as 33-year-old Robert Simpson and 27-year-old Ryan Preece.