Ms O'Neill was speaking after a meeting in Belfast on Tuesday.
It was attended by the Ulster Farmers Union (UFU), the Northern Ireland Agricultural Producers Association (NIAPA), banks and dairy processors.
Ms O'Neill said a "collaborative approach" was needed.
She stressed that support for "dairy farmers in difficulty must be prioritised".
"While I understand farmers' frustration at the current situation and believe that everyone has the right to peaceful protest within the law, I am convinced that we can better tackle these challenges if we work together," she added.
"That means producers, processors, banks and all politicians, not just here but in Westminster and in Europe as well, each playing their part.
"That is why I invited dairy sector representatives and the banks to meet me.
"I have been encouraged by their determination and commitment to work through this severe downturn."
Ms O'Neill said she was "encouraging our local banks to be as flexible and understanding as possible".
She said European action on raising intervention price thresholds was required and that she was determined to highlight the issue in Brussels and London.
Retailers in Northern Ireland have defended supermarkets' milk pricing policy after protests by farmers over what they get paid for their product.
Farmers staged a blockade at two stores in County Londonderry on Thursday and cleared milk from shelves at an Asda store in County Tyrone on Friday.
They also held protests at three supermarkets in Coleraine, County Londonderry, on Monday night.
Agriculture Minister Michelle O'Neill has said she expects every effort to be made to address the concerns of those Northern Ireland farmers affected by the drop in milk prices.