They cleared the shelves at Morrisons in Bideford, Devon, and Bude, Cornwall, then demonstrated outside with a cow.
The farmers say Morrisons pays as little as 74p for four pints, which they argue is far too low.
The supermarket chain said it had already agreed not to accept further cost price decreases from suppliers.
The protest is one of several that have been staged across the UK in the past few days.
‘Mission accomplished’
Michael Shadwick, who led the action in Bude, said store staff had been «overwhelmed» at what they did.
«We cleared the lot and yeah they’re left with none now, so it’s mission accomplished for us,» he said.
«Hopefully, the message will get back to their buyers that, you know, they need to support us.»
He described Morrisons as «one of the main culprits we’ve been told to target»:
«There’s no reason why they should be using the money that should be going to pay our bills to prop up their loss leaders and get footfall,» he said.
Milk prices have been falling as there is more supply than demand.
Darren Blackhurst, Morrisons group commercial director, said: «We try to pass on lower prices to our customers wherever possible. We do recognise however, due to reduced global demand, that this has created an oversupply of British milk, creating difficult conditions for many dairy farmers at present.
«At a constructive meeting on Wednesday with the NFU Dairy Board chairman, we confirmed that Morrisons is not accepting any further cost price decreases from our suppliers driven by the falling farm gate milk price,» he said.
Dairy farmer Chris Bellairs said the protest had «felt brilliant».
«Eighteen months ago we were getting 10p a litre more than what we’re getting now. That’s about a 32% reduction in what we’re getting.»
Source: BBC