Speaking to reporters at Britain's National Farmers' Union (NFU) annual conference, Fischer Boel said the move could give some producers an edge when broader reforms start to bite.
"I think, personally, that the transfer of quotas will be necessary one way or the other to ensure that the EU sugar industry remains competitive," Fischer Boel said.
In a speech, the Danish-born farm chief called on member states to urgently step up efforts to agree a consensus on all reform options.
"The existing sugar regime ends on July 1, 2006. If no decisions are made by then, we'll have no common agreement on sugar from there on. I don't mean to say that as a threat, but it is a fact," Fischer Boel said.
To date, the EU's long-awaited plans to shake up the regime, which has remained largely untouched since its inception in the 1960s, has called for massive cuts in the internal EU sugar price and annual production quotas.
Britain's NFU wants production quotas be easily transferable between member states so that the savviest producers benefit most.
"We have an efficient industry in this country. We need to make sure it's the competitive countries that benefit most," NFU president Tim Bennett said.
However, observers say the EU could be in for a bumpy ride in introducing moveable quotas.
Critics, especially in EU countries producing smaller volumes of sugar, say this could lead to domination of a few big producers like France, Germany and Britain.
Fischer Boel ruled out giving special concessions for a group of developing countries seen hardest hit by the planned shake-up of the bloc's sugar market regime.
She said the group of least developed countries (LDCs), which includes 49 mainly African and Asian nations and where sugar is often a vital export, would have to learn to adjust.
Under their "Everything But Arms" pact with the European Union, many LDCs have since 2001 enjoyed trade benefits with the 25-member club, allowing them to export sugar under an annual quota and at reduced-duty rates. *
"In recent months, much as been said about the idea of introducing import quotas for the Everything But Arms countries. I am not alone in the Commission in thinking that such a change in the agreement with these poorer countries is not an option," Fischer Boel told delegates.
"Re-opening this agreement would give out a wrong signal when the community is trying to convince the rest of the developed world to follow the EU example," she said.
The EU Commission is expected this spring to detail its plans to reform its protected and subsidised sugar market scheme, which has been accused of distorting trade and harming Third World producers.
It hopes to be moving toward a final agreement before the end of the year.