On Saturday, the global environmental group said it will go ahead with plans to sink nearly 180 boulders weighing between one to three tonnes.
"The actions foreseen by Greenpeace rest on confrontation and unilateralism, which risks threatening necessary cooperation," the Swedish agriculture and fisheries minister Eskil Erlandsson wrote in Dagens Nyheter newspaper.
"My hope is that Greenpeace will renounce such action and that instead we solve problems together," he said.
But, speaking to AFP, Greenpeace spokesman Staffan Danielsson said the Swedish government was taking cod "hostage" by not looking at the wider implications of bottom trawling on the environment.
"The cod in the Kattegat is severely depleted, it's in very bad shape, but there are other things in the oceans as well," he said.
"We have marine biodiversity (at the seabed) such as reeds, sandbanks, seabirds, corals, algae forests" that need protection from bottom trawling, which critics say disturbs the sea bottom and harms the maritime environment.
The boulders are to be sunk in zones classified as Natura 2000 in the Lilla Middelgrund (179 square kilometres, 70 square miles) and Flauden (104 square kilometres, 40 square miles) areas.
Both sites lie about 20 kilometres (15 miles) from Varberg port, off Sweden's southwest coast.
Natura 2000 is a network of sites around the European Union protected by EU directives aimed at protecting wildlife and their habitats.
Carrying out Monday's mission will be two Greenpeace vessels - the Beluga II and the Fehn Coast - with about 30 people on board.
"This is a conservation measure in order to protect habitats, which is what governments are supposed to do," Danielsson said.
A similar initiative was taken last year off Germany, and according to Greenpeace it has proven effective in discouraging fishing.