Board member of the Roads and Transport Authority Mohammed Obaid Al Mulla told the 7Days news provider that plans for two separate lines for passengers and freight transport are still set to go ahead.
His comments come after Richard Bowker, chief executive of Etihad Rail, suggested that only the freight line was to be constructed.
According to the news source, plans have been redesigned however, reducing rail track from 1,500km to 1,200km, with freight operations commencing from 2013.
The issue arises ahead of a major public transport forum to be held in Dubai next month (April), in which transport ministers and heads of city metro networks from around the world will gather.
Set to star at the event will be the launch of a 'superbus' prototype, running at 250km per hour.