Pike anglers are passionate about retaining livebating, but the majority of fishing groups want it banned, Scottish MPs were told during the latest debate on the Fisheries and Aquaculture Bill.
Conservatives and Scottish National Party members tried to introduce ammendments which would have allowed livebaits caught on the day, on the same water to be used.
But Scotland's deputy environment minister Sarah Boyack said: "After many stakeholders voiced concern about the risk of adverse effects on biodiversity in our inland waters as a result of unused live bait, we decided to include the provision in the bill, to make the policy clear.
"I acknowledge that pike anglers in particular, who represent a minority of anglers, have passionately expressed the view that the use of live vertebrates as bait should continue."
The Scottish Federation for Coarse Angling, the Pike Anglers Alliance and the Pike Anglers Club had all defended the method.
But Ms Boyack went on: ""I want to scotch a few myths that have arisen. The first is that this is a late Executive amendment, which we are trying to sneak through. It is not. The genesis of the proposal that is contained in the amendment was in the Executive's green paper,
"The second myth is that the ban is a welfare issue and that perhaps the next step would be to ban maggots or worms, if not fishing itself.
"I want to make our position clear and put it on the record. The Executive has been consistent on the issue from day one. The issue here is one of biodiversity. Introduced fish can compete with, predate on, give parasites to and spread disease among native fish. The Executive is totally supportive of angling as a sport and a recreation. That needs to be said, given some of the rumours that have been flying around.
"The third myth is that using live vertebrates as bait is not a problem. We do not agree with that view. The use of live vertebrates as bait has resulted in the translocation of live fish. That can happen when live fish used as bait are brought in from other sources and at the end of the day are discarded into the water being fished if they are not used."
Ms Boyack said the presence of Ruffe in Loch Lomond was proof that anglers translocating livebaits had caused alien species to be introduced to waters.
"Loch Lomond now supports a number of fish species that are new to the loch," she said. "One of those species, the ruff, is now the most common in the loch and is thought to pose a major threat to the loch's indigenous powan, which is an internationally renowned species of freshwater fish found in Loch Lomond and Loch Eck. The powan is listed in annex V of the habitats directive, so it is a fish that we want to protect.
It is the Executive's strong view that the use of lures and dead fish, often marine species such as sprat or mackerel, gives anglers a range of different methods that provide a perfectly acceptable alternative to the use of live fish.
"There is no need to put biodiversity at risk. I remind the committee that support for the use of live vertebrates is a minority view. It is a powerful view and it is held with passion, but support for a ban was and continues to be widespread.
"I believe that the case for prohibition is compelling. Support for prohibition is clearly the view of the substantial majority of anglers."
The bill will now go to a final reading, at a date to be fixed. Pike anglers on both sides of the border are lobbying for the amendments to be reinstated when it does.
For the debate in full click here.