"The phrase 'whichever changing room they feel comfortable with' puts women and girls at risk from predatory men."
The department store's response comes after Jean filmed herself visiting the branch in Sheffield last Sunday where she asked an employee if she could go into the men's changing rooms.
A manager at that branch reportedly told Jean men were not allowed to go into the women's changing rooms.
Jean then asked the manager when the policy had changed as a staff member in another department did not tell of this.
A spokeswoman for John Lewis said the gender-neutral policy was "not a recent change" as it had been in place "for a number of years".
She added in her statement to The Sun Online: "As an inclusive business, our customers are welcome to use whichever fitting room makes them feel the most comfortable.
"When developing any shop policy, we always consult with relevant stakeholders across the business and, where appropriate, outside of our business.
"When it comes to putting policy into practice, as a co-owned business we ensure that all of our Partners understand their responsibilities and exercise their judgment appropriately.
"Regardless of specific policy, if any customer were to act inappropriately, the necessary action would be taken."
This is what John Lewis told Jean in an email Credit: Twitter Jean asked John Lewis to clarify their position on gender-neutral changing rooms Credit: Twitter