The government will lobby the EU to increase fishing quotas in a bid to reduce the number of healthy fish being thrown back into the school.
The EU sets strict quotas for the number of each species of fish trawlers can bring back to port in a bid to prevent over-fishing of protected stocks such as cod.
Fisherman, however, complain these quotas mean they are having to throw back surplus fish, with as much as 60 per cent of catches going back into the sea.
Speaking to BBC Radio 4's Today programme this morning, fisheries minister Jonathon Shaw said it was an "absolute waste" to throw good quality fish back into the seat to die and confirmed the government will be pushing for an increase to its quota.
EU quotas were introduced amid concerns of rapidly declining fish stocks.
In 1987, the UK was fishing 170,000 tonnes of cod a year, raising concerns stocks would soon be wiped out.
Under quotas, this has been cut to 20,000 a year. However, this has allowed cod stocks to replenish themselves, meaning fisherman are finding it easier to haul in large trawls, especially in mixed fisheries.
Greenpeace estimates that 186 million fish were caught in UK waters last year but fisherman were forced to throw away 117 million, equivalent to 63 per cent of the catch.
Speaking to the Today programme, spokesman Oliver Knowles said: "At a very basic level I think you can see why setting a maximum catch for each species would work, at least on paper; the problem is quota systems don't work where you have mixed fisheries and of course most of the fishing that takes place around the UK is in a mixed fishery."
Mr Shaw confirmed the UK government will press the EU for higher quotas.
Environmental groups, however, are concerned this will undo the progress achieved so far on replenishing cod stocks.
In a bid to ease concerns, Mr Shaw said any quota increase would be "modest".
He told the programme: "What is important is we have fish tomorrow as well as today. We have seen a recovery in cod in the North Sea in particular - now that is good news.
"So that is why we will be pressing the commission at the annual round in December for an increase in cod and hopefully that will help the fishermen."
The UK will need to convince EU fisheries commissioner Joe Borg before any changes to the quota can be agreed.
Today he said it was "immoral" to be discarding so many fish but said there was no clear solution.
Mr Shaw said the government is considering other options, including special nets that only catch a certain type of fish.
Environmentalists argue fishermen will have to avoid large areas of the North Sea in order to avoid over-fishing protected species.
Greenpeace called for a "new model of fisheries management".