She said: "There are too many boats chasing too few fish so sustainability must be what we are talking about.
Scottish National Party Leader John Swinney accused Rhona Brankin and the Scottish Executive of flying in the face of the democratic will of parliament by calling the debate after a defeat on the issue last week.
Ms Brankin reiterated her argument that a £27m decommissioning package for the Scottish fleet was the only effective way of replenishing white fish stocks.
As Ms Brankin arrived for the debate, she and fellow ministers were met by a demonstration by more than 50 fishermen outside the parliament.
Fishermen at some ports had agreed to a voluntary tie-up of their vessels amid concern that they were being forced to fish for immature haddock.
They reacted with fury last week when the executive refused to endorse compensation.
Opening the debate, Ms Brankin said the aid package announced last week was the biggest ever for the Scottish fishing industry, and demonstrated the executive's commitment to it.
The minister told MSPs that the large quantities of small haddock fishing grounds, many below the minimum landing size, posed a challenge to the management of natural resources but also offered hope for the future.
She said: "There are too many boats chasing too few fish so sustainability must be what we are talking about.
"We have to reduce the capacity of our fishing fleet to allow stocks to increase. If we achieve sustainable stocks, we achieve a viable industry," she said.
At the heart of the £27m package was a £25m scheme for decommissioning to remove 20% of the capacity of the Scottish white fish fleet, the minister said.
She told MSPs the investment had been sought by the Scottish Fishermen's Federation and had been delivered in full.
In clashes with Scottish National Party fisheries spokesman Richard Lochhead, Ms Brankin said the executive stance was based on the best scientific advice.
She said no fisherman wanted long-term tie-ups and fishermen wanted to get back fishing.
Mr Swinney insisted that the minister bring forward an immediate tie-up scheme.
He said: "The minister said this was a debate about the coastal communities of Scotland.
"I think therefore the minister might have been better served in giving her scientific evidence if she had given some respect to the attitudes of fishermen."
Moving an amendment to the executive's motion endorsing its package, Mr Swinney said: "The debate is also about the will of parliament."
Mr Swinney referred to last week's events and his party and others had sought answers and action from the executive.
Commenting on the minister's refusal to implement last week's vote, he said: "What does that say about the respect of this executive to this democratic Scottish Parliament?
"The problem was that the executive could not command a majority and now the minister tells us that the executive is having regard to and is listening to the parliament.
"We are not interested in them having regard to and listening to the parliament.
"We are interested in the government coming here and telling us how they will implement the will of parliament."
'Spurned and ignored'
Tory fisheries spokesman Jamie McGrigor said fishermen wanted sensible and decisive action and wanted it now.
He described last Thursday's vote as a victory for the fishing industry but criticised an "embarrassed" executive for trying to overturn the decision.
He said: "This parliament made a decision last Thursday which the executive spurned and ignored.
"We are back here again to debate the same debate and I don't think yet more words on this issue will be any comfort at all to fishermen and their families who depend on the industry for their livelihoods."
For ministers in the Labour/Liberal Democrat coalition, Lib Dem votes were once again expected to be critical on Thursday.
Tavish Scott, who resigned his junior ministerial post following last week's vote, said he would be voting against the executive.
However, the rest of his group, including last week's rebels, were expected to support the executive, therefore overturning last week's vote.