Is there a row brewing between the Treasury and Transport?

Are the Department of Transport and the Treasury at loggerheads over the issue of fuel duty versus road pricing? That certainly seems to be the implication in a response from Stephen Ladyman on the matter.

The Tory MP, Anne McIntosh asked the Transport minister what assessment had been made on the "likely effect on congestion of increases in fuel duty". Stephen Ladyman's response was that responsibility for making such impact assesments was the Chancellors, but went on to say that "raising fuel duty would be significantly less efficient than road pricing as a means of reducing congestion".

Given that Gordon Brown claimed his recent increase in fuel duty was about the environment and congestion it's certainly interesting that the Department of Transport is so willing to state that he's wrong. I wonder if Ladyman was speaking for wee Doogie in his answer?