About 25 boats fish for sole, flounder, turbot and brill in the fisheries area from the Clarence River, on the Kaikoura coast, to Fiordland.
Two years ago, the quota was almost halved and local fishermen and processors have been campaigning to have it increased ever since.
The quota for the 2009-10 year, which finishes in September, is 1617 tonnes, of which 1430 tonnes is available to commercial fishers.
Harbour Fisheries owner Aaron Cooper's Dunedin company processes much of the flatfish caught off the east coast.
He said the ministry approved a top-up quota of about 300 tonnes mid-season last year and the industry hoped for another increase this year.
But he said the ministry seemed in no hurry to make a decision, despite letters, emails and telephone calls from him and others since the start of the year.
The ministry rejected that claim, saying it was assessing the scientific data to see whether an increase was sustainable.
If it was, a decision could be made by May or June.
But Mr Cooper and others said that was too late, as it did not leave fishermen enough time to catch fish before season ended.
Catches and markets had been good this season and fishermen were keen to be able to catch more, he said.
Monthly records showed catches were already about 100 tonnes ahead of the corresponding date last season, Mr Cooper said, predicting boats would run out of quota well before the end of September, unless an increase was approved.
Some would have to tie up, he said, although others would soon be able to begin catching rock lobster.
However, the rock lobster prospects had also been affected by the ministry's decision last week to halve the 2010-11 quota for the Otago fisheries area from 209 tonnes to 104 tonnes.
Bluewater Products owner Ross Hutchison, who owns flatfish quota and processes catches at his Dunedin factory, said he had begun instructing his fishermen not to go to sea as often because catches were so abundant his quota limit would be met well before September.
That was not good for the industry, as a steady supply of fresh fish throughout the year resulted in the best prices at market, he said.
Ant Smith, a 23-year veteran fisherman working out of Port Chalmers, said he had real concerns crew would leave the industry for other jobs if boats had to tie up, as they did not get paid unless catches were landed.
"They don't want to leave, but they have to pay their bills."
Uncertainty over the flatfish quota and the cut in the crayfish quota might also send some smaller operators to the wall, he said.
"All this is really hurting the smaller guys."
Ministry of Fisheries inshore fisheries manager Leigh Mitchell said the ministry was "diligently working" on whether the flatfish quota could be increased.
Many flatfish species were relatively short-lived and their numbers varied markedly from year to year.
Research was being done to assess the abundance of species this year and whether an increase was warranted.
Increases were not automatic, she said.
Even if a mid-season increase was approved, the quota would revert to its baseline at the start of the 2010-11 season.
