"I'm not saying it is not going to happen, it is just not going to happen in a heartbeat.
"The ratepayer of Auckland needs to know what they are on the hook for, because central Government is not going to pay for it."
Mr Key's comments are the latest shot in a series of clashes between the Government and Mr Brown over the merits of the rail loop and the second time in a month that Wellington has expressed a concern about the Auckland Plan.
Several Cabinet ministers chastised councillors over the compact city model promoted in the plan, claiming it would force land and housing prices up.
They wanted it abolished, or at least made more flexible.
Mr Key and Transport Minister Steven Joyce's concerns about the rail loop are making it difficult for Mr Brown.
Last night, Mr Brown played down Mr Key's comments as nothing new, and said his thoughts on the timeline for the rail loop had not changed.