The consultation, which closes December 17, 2008, represents the response to this summer's Gallagher Review, which recommended a more cautious approach to promoting biofuels because of concerns about their social and environmental side-effects
The plan under consultation from today includes slowing the annual increase in renewable transport fuel targets to 0.5% each year.
This would see the target under the Renewable Transport Fuel Obligation (RTFO) rising to 5% in 2013/14, rather than in 2010/11 as in current plans.
Launching the consultation, Mr Adonis said: "Everyone agrees that to tackle climate change we must develop new and cleaner fuels. But we are clear that biofuels will only have a role to play in this if they are sustainably produced."
Within the consultation, the government said it wants to add biobutanol and hydrogenated renewable diesel to the list of renewable fuels that qualify under the RTFO, which requires all companies that supply more than 450,000 litres of petrol or diesel to UK forecourts to include proportions of renewable fuel within their supplied products.
The Department for Transport said it is still supporting the proposed European target of 10% renewable transport fuels by 2020, as being negotiated within the forthcoming Renewable Energy Directive.
But, contradicting its statement of support, the Department said the 10% target was "not presently justified by the scientific evidence" and would only be possible if new controls on land use change were enforced globally.
Transport ministers want the target to be kept open to review should new evidence emerge on the impacts of biofuels.
In the mean time, the government said sustainability criteria for biofuels are being negotiated and should address indirect as well as direct effects on land use, while the government said it aims to help draw up international standards and controls on biofuels "which reflect the international nature of the biofuels industry".
As well as the immediate changes to the RTFO targets, which will be pushed through Parliament within the Renewable Transport Fuels Obligation (Amendment) Order 2009, today's consultation also poses some "long-term" policy questions.
The government is seeking views on issues that could help shape future UK biofuels policies, including support for using tallow as a biofuel, and how to encourage more production of second-generation biofuels - biofuels made from non-food crops.
Europe's draft Renewable Energy Directive suggests double rewards for biofuels from non-food sources, and the government in the UK also believes "we should aim to target support on the development of lower carbon and other so called ‘second generation' biofuels".
Further questions within the consultation ask for views on whether to split the RTFO to introduce quotas for first generation biofuels and separate targets for other renewable fuels. And, the government is looking into how to link the RTFO targets to carbon emissions savings achieved by biofuels, in order to encourage efficient production processes.
Alongside the biofuels consultation today, the Department also announced a new £6 million injection of funding into research the Carbon Trust is carrying out into developing advanced biofuels.
Mr Adonis said: "We need to take a more cautious approach to biofuels and today's consultation sets out our options, as well as dedicating a further £6 million to helping ensure that second generation biofuels are truly sustainable."