The closing date has been extended by two weeks to 2 January next year.
The Agency has proposed abandoning application, variation and surrender fees in favour of levying subsistence charges alone from 2009/10. The aim is to reduce the administration involved in collecting the fees.
It estimates that charges to business as a whole will be reduced by 17%, with only a dozen firms facing increases.
Charges would be set to the type of permit condition attached to a discharge, with a fee levied for each one. The lowest fee, at £65 a year, would be for discharges with only descriptive conditions set. This rises to £220 for those with numerical limits on pH, temperature and certain other factors. Discharges with permit conditions for biochemical oxygen demand or ammonia would be charged at £750 per annum. Any other permit conditions would attract the highest fee of £2,250.