In particular, the ministry said Pike River failed to ensure proper ventilation and methane gas control, and said the company should have placed the main ventilation fan outside the mine.
Pike River Coal indicated last month that it would not be defending the charges.
Judge Farish today found all nine charges proved and entered convictions against the company.
The judge specifically found the breaches by Pike River Coal was "causative of the explosion and the subsequent deaths of those men who perished".
A detailed and lengthy judgment will be made available in 14 days. Sentencing is scheduled for July 4 and 5 in Greymouth.
In a statement released this afternoon, Pike River Coal Ltd receivers PricewaterhouseCoopers said they had no comment on the judgment, but would assist the court in sentencing in July.
PwC partner John Fisk said the matters had all occurred prior to the receivers' appointment, and PwC had advised the court in July last year that the receivers would not defend charges against the company.
"Given the amounts owing to creditors, the receivers did not consider it in the economic interest of creditors to spend the limited funds available to the company on any defences to the charges. This was a pragmatic decision in the circumstances.
"The receivers therefore did not participate in the formal proof hearing against PRCL in March this year, and have no comment to make on the judgment against PRCL."
At sentencing in July, the receivers would provide information to the court and prosecution in relation to the company's financial position and current status in order to assist the court.
"The receivers do not intend to take any position in relation to what may be an appropriate sentence. This is a matter for the court," Mr Fisk said.
The Ministry of Business Innovation and Employment said the convictions followed a year-long investigation by up to 15 investigators.
"The former Department of Labour charged three parties under the Health and Safety in Employment Act over the explosion which killed 29 men in November 2010,'' High Hazards and Specialist Services general manager Brett Murray said.
VLI Drilling Pty Limited (of Australia) was convicted on three charges and in October last year, was fined $46,800.
The third case against the former Pike River chief executive Peter Whittall has still to be heard.
Mr Whittall has applied to have his case heard outside of Greymouth citing fears he may not receive a fair hearing on the West Coast.