Police were seeking witnesses, Mr Hill said.
A police spokesperson said now the matter was before the courts police would not be making any further comment.
Store owner Jass Narsey said his two staff members, including one who allegedly had a pistol brandished at him had been left badly shaken.
"I have owned this store for 16 years, and this is the first time like this has happened. But I have always feared it would happen one day," he said.
"Fortunately my staff members are coping okay but it has been a bit traumatic for them. I'm so thankful they were not hurt," he said.
The 16-year-old youth was due to appear in Tauranga Youth Court today. Anyone who has any information is urged to call Tauranga police on 577 4300 or alternatively call the Crimestoppers line anonymously on 0800 555 111.