According to China's Xinhua news agency, investigators found that the rains had caused a nearby river to breach its banks, but that the mines were poorly prepared for an accident.
The flooding "exposed prominent problems in workplace safety and accident prevention among local governments, agencies and enterprises in facing a serious natural disaster," said a report posted on the website of China's workplace safety agency.
China's coal mines are the deadliest in the world, recording more than 3,800 fatalities in its mines last year – an average of about 10 deaths a day.
However, labour rights groups say the real death toll is likely much higher with mine operators covering up accidents to avoid official attention.
With China reliant on coal for about 70 per cent of its booming economy's energy needs, the soaring demand for coal means many mine owners are willing to cut corners in the quest for quick profits.
In addition to the six people to be prosecuted for the Shandong mine floods, Xinhua said another 20 people, many of them officials, faced demerits or other unspecified penalties.