The suspension has been enforced even though the charity itself had previously described the town as "squalid and run-down".
Sue Nelson, who has worked for Encams for four years, made her off-the-cuff comment at a London conference last week. She sparked an outcry from the town's residents and has since been suspended on full pay pending an investigation, which could lead to disciplinary action.
The charity insisted that it must learn from the incident and reassess the way that it gets its messages across, but denied that increased political correctness would censor any future messages.
"We need to be sensitive to people's feelings," said Encams spokesman Peter Gibson. "But I wouldn't want us to lose the hard-hitting nature of what we do."
Gibson admitted that Nelson's comment was probably an inappropriate joke that meant no harm. "The last thing she would want to do is upset people," he said. "The issue is with the terminology used."
Encams, which is located on Wigan Pier, has itself previously questioned the town's environment. In a campaign about towns with a graffiti problem, the charity said: "Wigan is among the worst" with "racist messages scrawled across walls on the railway line". It went on to say that "graffiti adds to the sense of squalor and makes people feel unsafe".
In another statement the charity said "fly-posting makes our town look squalid and run down".
The charity admits making the statements, but says that, unlike Nelson's comments, they did not impact negatively on the people of the town. "Nelson's comments are in no way representative of what we feel about the town or the people of Wigan," said Gibson.
He added that Wigan is much improved, and is leading the way with initiatives such as a recent 30-day clean-up involving residents and businesses, and a system for fining people who drop litter.