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The scheme, which has the potential to create thousands of local jobs - including many in the construction sector - is proposed for the Sprucefield shopping complex, outside Lisburn.
Plans for the development have been public knowledge for the last four years.
However, it has faced continued wrangling, both political and commercial.
Environment Minister Sammy Wilson today said: "I have considered the options available to me and I am satisfied that the best way forward is through the public inquiry procedure.
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"In making this decision I am conscious of the importance of new inward investment and the potential for employment associated with the proposal, particularly in the current economic climate.
"I will therefore be asking the Planning Appeals Commission to give this matter a high priority."
Joint venture partners Westfield and Snoddon Developments have welcomed the Minister's move.
They submitted a fresh planning application to Lisburn City Council last year.
The revamped proposals saw the number of auxiliary shops based at the complex slashed, from 29 to 19.
Last August, the developers said they expected the scaled-down plans, which stretch over 50,000 square metres, to overcome objections from concerned retail groups.
Initial proposals for the Sprucefield scheme were lodged and approved in 2005.
However, the then minister Lord Rooker's decision was overturned at a judicial review.
Retailers in Belfast, Lisburn, Banbridge and Craigavon voiced strong opposition to the plans.
The pressure groups said they did not oppose a John Lewis outlet, rather the size of the development and the number of subsequent stores associated with the project.
(PR/JM)
