She said there had been some movement in the numbers but it's "not enough for us".
She talked up Government policies which aim to reduce the gap, such as a boost to the minimum wage.
"Women are over-represented in the number [of people] earning a minimum wage," she said and added that the policy would help close the gap.
Recent pay equity settlements for female-dominated professions, such as nurses and teachers, would also help Ardern said.
But she said there would always be a lag between the Government's action, and what comes through in Stats NZ's numbers.
Women's Minister Julie Anne Genter agreed with Ardern and said it was "going to take time" to bring the gender pay gap down.
She said the Government wanted to see a lot more change as "there is a lot more that needs to be done to close it further".
Stats NZ's Labour market statistics manager Scott Ussher said although the pay gap has remained flat since 2017, it has been trending down since 1998 when the gap was 16.2 per cent.
The data showed that women's median hourly earnings from salaries and wages increased $0.75 (3.2 per cent) since the June 2018 quarter, to $24.50 in the June 2019 quarter.
For men, the median increased $0.85 (3.3 per cent) over the same period to reach $27.00.
"The gender pay gap is a useful measure when trying to understand differences in pay between men and women, due to its simplicity. But this measure is limited," Ussher said.
"It doesn't account for men and women doing different jobs or working different hours. It also doesn't account for personal characteristics that can influence pay, such as qualifications and age."
For example, Ussher said the gender pay gap is smaller for people younger than 30 years.