Plans to knock down Huddersfield Royal Infirmary and centralise A&E services in Halifax could be scrapped after Jeremy Hunt asked NHS bosses to reconsider.
The proposals, which involve replacing Huddersfield's hospital with a smaller site, sparked protests and raised safety concerns over longer journey times to hospital.
The shake-up was referred to Mr Hunt by Calderdale and Huddersfield joint health scrutiny committee last summer and an independent review was carried out.
The official findings of the Independent Reconfiguration Panel (IRP) have not yet been made public.
But in a letter to the scrutiny committee, Mr Hunt said the IRP had "observed a wide variety of failings which call into question the benefits of this scheme and the way in which the process has been managed so far."
Mr Hunt said the IRP found a "lack of consistency" with the proposals, and "scepticism about whether proposals of this scale and complexity are actually deliverable."
The proposals involve an expansion of NHS services at a bigger hospital in Halifax, more planned procedures being carried out at a new facility in Huddersfield and more services being offered outside of hospitals.
The new Huddersfield hospital was originally planned to have 120 beds, but that was reduced to 64.
Mr Hunt said there were concerns over the delivery of out-of-hospital services and whether the overall reduction in hospital beds was justified.
He said it was also not clear that capital funding for the project would be available.
He said: "In short, the proposals are not in the best interests of the people of Calderdale and Greater Huddersfield and I would ask the NHS locally and nationally to reconsider."
He said the independent panel was of the view that further action was required before a final decision on the proposals is made.
The hospital proposals are also subject to a legal challenge after NHS campaigners launched a judicial review.