A significant proportion of the debt accumulated during this period could be attributed to price inflation for dairy land, which averaged 12 per cent a year.
Because demand for such land exceeded available supply, much of the debt was reflected in higher land prices.
"This has left a significant number of dairy farmers vulnerable to a fall in the milk price or a decline in land prices," the ministry said.
This year's drought had increased the vulnerability of most North Island dairy farmers by reducing milk revenues and increasing feed and pasture renewal costs.
Dairy NZ estimates that nearly 40 per cent of North Island dairy farmers will not be able to meet their working expenses and interest costs this season because of the effects of the drought.
An expected higher milk payout this season would assist farmers to service their debt, the ministry said.
"Unfortunately, some of the most heavily indebted dairy farmers may have difficulty in servicing their debt even with the higher payout," it said.
Looking ahead, debt would remain a risk to the financial viability of many dairy farmers, the ministry said.
The main dairy co-operatives have increased the farmgate milk price forecasts for the season ahead.
Fonterra has announced an opening forecast farmgate milk price of $7 per kg of milk solids for the 2013/14 season - up $1.20 on the 2012/13 season.