Sail in Greece boss Alexander Nastos admitted there had been problems with communication and the quality of the boat.He told the Herald the boat and the tour manager had been replaced.
"It is true that we faced a problem with the toilets," he said.
"Some of the travellers dropped toilet paper on the boat and the pipes blocked and as a result we had sewage coming out of the pipes. We have already changed our boat for the upcoming tours."
Mr Nastos said the company was giving full or partial refunds to everyone who had contacted them.
"Look, when you have an issue on the boat most people will be unhappy with it," he said.
"Bad issues can happen and our company took immediate actions to resolve them. However the people on the Kiwis in London post are blaming the company even if we have already refunded the people."
He said a claim the cruise was overbooked was not true and believed his company was being targeted by a rival cruise operator, linked to the Kiwis in London page, who wanted to make the incident "seem much worse" than it was.
However following further correspondence with the Herald Mr Nastos said he wished to retract these claims.
Kiwis in London administrator Clint Heine said there was no truth to what Mr Nastos had said.
"Kiwis in London works with over 2 dozen established travel companies and advocates for almost 50,000 Kiwis and other expats living in London," he told the Herald.
"Our community brought this issue to our attention and as a result of the publicity on our page, Sail Greece has refunded all customers who were affected in this. No expat traveller should expect conditions like this when buying travel products and we will carefully watch Sail Greece with their future trips to ensure Kiwis are well looked after."