The first two received positive results, but he said "something funny" occurred during acidic testing when the milk was left outside - milk in the triple layer bottle degraded faster.
Fonterra launched the triple-layer Anchor bottle in March, saying it protects milk from light and keeps it fresher and tasting better for longer.
Tristan's project has been praised by University of Auckland and Fonterra scientists, and he now plans to carry out further repetitions of the experiment.
Fonterra scientist and brands innovation manager Olaf van Daalen said the work was of a very high calibre.
However, Mr Van Daalen said the co-operative's own testing had shown the rate of temperature change in the old and new bottles was exactly the same.
"Even a very small difference in the starting condition of the milk will make a big difference to how quickly it degrades.
"Tristan acknowledges this himself in his report, noting that bacteria may have entered the bottle when he opened the cap for PH testing."
Professor Conrad Perera of the University of Auckland's School of Chemical Studies said the experiment would need to be repeated a number of times to draw any conclusions.
It was possible the bottles were not properly sterilised, and if that was the case it would explain the difference in acidity.
"The budding scientist needs to be congratulated and encouraged for his enthusiasm and enterprise ... we hope he will think of doing food science when he is ready to enter the university."
Tristan previously featured in the Herald when, as a 10-year-old, he top-scored in an international Cambridge mathematics exam usually sat by students in Year 11.
He plans to eventually work in the science research field, most likely in quantum physics or medicine.
He is still in Year 7, meaning his Cambridge studies - he will sit Year 11-level physics and English exams this year too - are mostly done outside school hours.
Thomas Pang, Tristan's father, said his son had always taught himself advanced lessons, so much so that they sometimes had to rein him in.
"Initially he wanted to do [university entrance] physics this year, but we actually stopped him - we don't want to blow his little brain."
Tristan's and other winning entries will be displayed at Motat this week.