Property developers, Corbo, launched a planning application to build the shopping centre last week, the BBC reports.
In order to complete the project, however, the company needs to purchase two playing fields near the site.
These sites are owned by the Christian Brothers, who have claimed they were not consulted over the application and will not sell.
A spokesperson for Corbo said they were "surprised" commercial agents acting on behalf of the Christian Brothers had written to the Planning Service expressing that view.
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Last week the company's chief executive, Stephen Kirkpatrick, said they had had "detailed discussions with the church bodies that own the two playing fields".
The president of the Omagh Chamber of Commerce, Gerard O'Hanlon, said he hopes both parties can resolve their differences.
"When the shopping centre was announced for the Scotts Mills site and the playing fields the businesses in Omagh town centre were very excited about it," he said.
"It would be good to see that development, it would be good to secure business for the town centre and making Omagh a vibrant town centre and maintaining jobs."
The £200m scheme would create up to 800 jobs during the construction phase, with more than 1,500 full-time positions created upon completion.
The development would include a major food store and an 800,000 sq ft shopping mall with a seven-screen cinema and bowling alley.
(NS/BMcc)
