A spokesman for the city council said last night: "There is no question of any personal differences between Sir David and Neil Scales.
"As chief executive, Sir David is carrying out the policy of the city council and is doing all he can to help deliver a tram system for Liverpool.
"He will be meeting Neil Scales as soon as possible to help make sure the tram is delivered on time and on budget."
John Lennon Airport is currently due to be served by Line Three of Merseytram with completion by 2010.
A change to the route proposed by the council - via the loop line through Belle Vale, Halewood and Garston - could not be completed until at least 2012, one bidder has claimed.
The two consortia left in the running are the Met group of Keolis/Parsons Brinkerhoff/Balfour Beattie and the M-Tram team of Serco, Mitsubishi and MTR Corporation.