Discussions over the Rossington scheme in South Yorkshire have included charging car drivers to use a new road in a bid to persuade them to take the bus instead, although no firm plans have been drawn up yet.

Documents obtained under the Freedom of Information Act reveal officials at the Department for Communities and Local Government (DCLG) marked down the bid, near Doncaster, in their initial assessment because of concerns mainly over transport.

Since the initial bid was submitted, the scheme has also been radically scaled down from 15,000 homes to about 5,000 so none of it is any longer on greenfield land.

The Government's eco-town project has been surrounded by controversy since its launch last year, with the Tories now openly opposed amid concern many of the shortlisted schemes are not truly environmentally friendly.

The Rossington bid – one of 13 on a Government shortlist to build up to 10 of the environmentally friendly new towns – appears to be the only possible site in Yorkshire after leaders in the Leeds City Region told the Government they could find no suitable location in their area.

Revised plans for the Rossington scheme – backed by a partnership including UK Coal, Persimmon, Helislough and UCL – will now see two neighbourhoods developed, mainly on land owned by UK Coal on the site of an old colliery, with about 5,000 homes, the smallest number to qualify to become an eco-town.

But DCLG's scoresheet of the initial plans reveals that although the content of the scheme was considered "very strong", the top ranking, transport was ranked only "medium" – the third of four possible rankings, and the lowest possible to still make it onto the shortlist.

A second analysis by several Government departments rated the scheme only C on a scale of A to F – meaning it met the eco-town criteria but there were "highly significant" issues which needed to be addressed –- while the scheme was rated only "medium" on a scale of how deliverable it was.

Moreover, pressure on housing affordability – one of the key drivers of building the eco-towns – is only considered "moderate" in the area, which is in Housing Minister Caroline Flint's constituency although she will take no part in the final decision on the scheme.

The Government's main concern appears to have been that the scheme would be too dependent on the building of the FARRRS link road from the M18 to Robin Hood Airport, raising fears it would be overly reliant on car travel instead of being truly environmentally friendly. The concern was echoed last month by a panel of experts set up by Ms Flint to assess the bids.

The documents obtained by the Yorkshire Post also reveal officials wrote to the Rossington Eco-Town Partnership earlier this year asking for alternative transport ideas "to ensure that sustainable travel would be an integral element of the scheme".

Now the scheme's architects are working up plans for a road linking the development with junction three of the M18, connecting it to Doncaster town centre, with the aim of making it a "high quality bus corridor". Among options to persuade people to use the bus include having toll lanes so cars – or lone drivers – pay to use the road or using traffic light timings to make travelling by bus far quicker than by car. "We're not saying to people you can't have a car," said Adrian Spawforth, managing director of Spawforths, scheme planning consultants. "We're designing it in such a way it will become your third or fourth choice because it's going to be a little harder to use it than to use the bus." He said the idea of imposing a toll for cars to use the road had been discussed. "We're not ruling anything out, we're not ruling anything in. Anything which encourages that modal shift has got to be considered." UK Coal said: "We believe by the time we've completed the re-engineering of the project it will tick all the boxes."

The Department for Communities and Local Government said: "Rossington is a strong proposal but there are challenges that developers need to address, as with all locations on the shortlist. No decisions have been taken on which bids will go forward and only the best ones with the highest environmental standards will be in with a chance of making the final shortlist."