The application for a nationally significant infrastructure project (NSIP) development consent order (DCO) was submitted to the Planning Inspectorate in September.
The Rail Central development, being promoted by Ashfield Land and Gazeley, is proposed for a site where the West Coast Main Line meets the Northampton Loop Line to the south west of Northampton, between the villages of Blisworth and Milton Malsor.
The scheme would have direct rail connections to the West Coast Main Line and Northampton Loop Line plus road access to the A43 and M1.
In addition, the proposals included up to 702,000 square metres of warehouse space; highway improvements to 15 junctions, with a major upgrade to junction 15A of the M1; and 26 hectares of ecological mitigation at land south of junction 15A.
Under DCO procedure, after the submission of an application, PINS has 28 days to consider whether to accept the application for examination.
But a letter published by PINS earlier this month said the body had decided not to allow the Rail Central application to progress to examination.
The letter said the secretary of state "considers that the application cannot be accepted as it is not of a standard that the secretary of state considers satisfactory".
The plans have now been resubmitted. PINS again has 28 days to consider whether to accept the application for examination.
PINS is already considering an application for a DCO for a rail freight scheme in Northamptonshire. The application, submitted by developer Roxhill in May, seeks consent for the Northampton Gateway scheme on 247 hectares of land to the west of the M1 near Wooton.
In August, separate plans for a rail freight interchange in the West Midlands were accepted for examination by PINS. The West Midlands Interchange would be built on a 297-hectare site about 10 kilometres north of Wolverhampton and six kilometres west of Cannock in Staffordshire.