The letter,, external from Labour leader of the council Nick Mannion and the deputy leader, independent Michael Gorman, said the authority had nine main areas of concern.
These included green belt protection, prioritising brownfield sites first and concerns about the proposal being brought forward without formal involvement of elected officials in the area.
A petition against the plans was presented to the House of Commons by Macclesfield MP Tim Roca last week.
The government is currently looking into all 12 areas put forward for a new town, with a decision set to be made in the spring.
A Ministry of Housing, Communities and Local Government spokesperson said: “Our landmark plan to build new towns will help restore the dream of homeownership for families across the country.
“We continue to work closely with local leaders to ensure these towns will be in the right places and have the necessary infrastructure.
“No final decisions will be made until the spring, however we recognise that there are clear strengths in all 12 of the sites recommended by the taskforce.”