Such cases were a rarity, Mr Warner added.
The father would be charged if police could identify him. The maximum penalty for statutory rape is 20 years in prison.
Child, Youth and Family were notified of underage pregnancies, he said.
But CYF regional director Sue Critchley would not confirm whether the organisation had investigated or taken any action in the case of the 13-year-old Tauranga girl, citing privacy concerns.
"Child, Youth and Family's focus would be on the safety and wellbeing of the young mum and her baby," she said.
"When cases like this are referred to Child, Youth and Family we assess if the young mum has good family support and whether there are any care and protection concerns for her or her child.
"If those supports are in place and both are safe and well there would be no need for Child, Youth and Family to be involved."
Family First national director Bob McCoskrie said any case of a 13-year-old becoming pregnant was a tragedy.
"Any pregnancy for a young teen is very difficult both physically and emotionally.
"Official statistics show that there were approximately 80 on average abortions for 11-14-year-olds each year, so a 13-year-old giving birth is a tragic reminder that we need to do more to prevent young people becoming sexually active."
Throughout the Bay of Plenty 51 girls under 16 years old gave birth between the start of 2008 and August 19 this year but the figures have dropped steadily from 12 in 2008 to five last year and three so far this year.
Mr McCoskrie said he was pleased the number of teen mothers was dropping.
"It does raise a number of issues including the fact that most people would be horrified that young teenagers are sexually active, have got pregnant, and the figures also wouldn't include girls who got pregnant but were sneaked off for an abortion without their parents knowing - as is allowed under the law," he said.
"We believe the downward trend, which is similar to the drop in abortions, is because of better information around pregnancy, fetal development and the consequences of sexual activity, which young people are now able to access via the internet."
Family Planning New Zealand chief executive Jackie Edmond said the Bay of Plenty figures reflected a global trend.
"Internationally the figures of unplanned pregnancies have dropped and that is because women are using longer-term forms of contraceptives like IUDs and implants. It figures that New Zealand's figures would drop as well."
Ms Edmond said it was unlikely longer-term forms of contraceptives were responsible for the drop in pregnancies in girls under 16 but was unsure what may have caused it.
The rate of abortions among girls under 16 was extremely low, with the highest abortion rate among women aged between 18 and 25, she said.
"The reality is most 16-year-olds haven't had sex. The reality is that it's far less common than you think," she said. "Obviously we all get very worried in terms of a 13-year-old or a 14-year-old having a baby but the numbers are really small, which is good."
Te Whakatipuranga School for Young Parents teacher in charge Phil Merritt said the youngest student he had taught in almost 13 years since the Tauranga programme started was 13.
"We don't get a lot of students that young but over time we've certainly had a few."
The teen parenting unit is run by Otumoetai College but held at the Bay of Plenty Polytechnic. It can cater for up to 35 young mums, usually between the ages of about 15 and 19, at any one time.
