The shopper took a photograph of the fouled toilet and posted on his Facebook page, resulting in a number of pun-filled comments.
"Everybody loves toilet humour and that's why it just went off," said the customer who later took the post down.
Alerted about the matter by the Herald on Sunday, a Mitre 10 spokeswoman confirmed the toilet shown in the Facebook post was at Mitre 10 MEGA Botany.
The store assistant manager had removed it immediately after becoming aware of its state following the inquiry.
"He was very shocked, just couldn't quite understand what happened. It's not something he's seen before," the spokeswoman said.
He had "wanted to just get it cleaned up straight away".
The spokeswoman confirmed the toilet - "not too far from the bathroom section but... sort of slightly off from the other toilets ... slightly hidden away" - appeared to have been fouled with faeces.
She said an investigation would be launched, including a review of CCTV footage.
The assistant store manager would be "following up... with his team members and looking to see what... they can do to make sure it doesn't happen again".
The spokeswoman, who had been with Mitre 10 for "a few years" had never heard of a similar occurence.