Eric Leighton, 18, was killed in an auto shop class at Mother Teresa High School.
He was cutting an empty oil drum in two when residual vapours exploded.
The charges fall under the Occupational Health and Safety Act and carry penalties of fines up to $500,000.
The school board is accused of failing to provide proper information and instruction, failing to take every reasonable safety precaution and failing to warn the teacher and student about potential hazards.
The ministry is conducting safety inspections of school woodworking and metalworking classes as well as auto shops and science labs across the province.
A spokesman said the ministry is working with the education department and school boards to ensure all schools have a thorough understanding of safety rules and regulations.