Cheshire West and Chester Council had refused planning permission for the new homes, along with public open space and associated highways and infrastructure works, in 2014.
Following an appeal, a planning inspector recommended that planning permission be granted subject to conditions.
A decision letter issued on behalf of the secretary of state this week said that he agreed with this conclusion.
The decision letter said that the appeal had been recovered by the secretary of state due to its size.
The letter said that Clark agreed with the inspector that the main consideration in the case was whether the proposal "would prejudice the achievement of a coordinated and sustainable form of development within the Winsford Station Quarter Urban Extension (SQUE)".
According to the inspector’s report, the Station Quarter Urban Extension has been identified by the local authority to include a mixed-use development of in the region of 1,000 new homes, to be "achieved through a comprehensively planned approach in line with an agreed development brief".
The letter said that the secretary of state acknowledged there was conflict with "policies in the development plan which seek an adopted development brief prior to granting permission for any scheme within the proposed SQUE."
However, it added that he found that "the degree of harm caused by allowing this appeal in advance of the development brief and in conflict with [local planning policies] would be very limited."
The letter added that Clark was "satisfied that the appeal scheme would not prejudice the achievement of a coordinated and sustainable form of development within the SQUE; it would bring forward significant market and affordable housing which would materially boost supply and this benefit is attributed significant weight."
"Overall, the secretary of state considers that, although the proposed development would pre-empt a comprehensive development brief for the SQUE, it represents a sustainable form of development which will provide much needed housing and which accords with the policies of the development plan and Framework taken as a whole", the letter concluded.