Dianne Gray was asked to give up her post pending an investigation from the Royal New Zealand Society for the Prevention of Cruelty to Animals after Waipa District Council found the dog-runs to be overcrowded and in squalid condition, the Waikato Times reported.
Volunteers had spent much of the week cleaning up the site and the council had made repeated warnings about the number of dogs at the site which was restricted to 20 dogs.
When council staff visited in March 37 dogs were found and in the past this number had been as high as 70.
Environmental services team leader Karl Tutty said "the amount of faeces, the number of flies and the odour" constituted a nuisance.
RNZSPCA head Robyn Kippenberger said the dogs were living in urine soaked cages and in "filthy" conditions.