Cross Roads Properties Ltd originally applied for land use consent to construct the Mega building at the Frankton Flats, associated car parking and landscaping, which was considered on direct referral to the Environment Court in September 2012.
It was heard in conjunction with an application from Foodstuffs South Island Ltd to establish a Pak'n Save supermarket on a nearby site.
Both applications were granted by the court last year.
In his decision, dated March 25, Judge Jon Jackson said in the case of the direct referral by Cross Roads, expenses incurred were generally recovered from the applicants seeking consent.
''Following negotiations, the registrar and Cross Roads Properties Ltd have agreed that a sum of $50,000 (including GST) is an appropriate amount to be recovered in relation to the expenses incurred by the court for this proceeding.''
Costs included the actual cost and time taken in relation to administration, case management, hearing and final determination and related disbursements, including venue hire.
H&J Smith managing director Jason Smith told the Otago Daily Times last week work on the Mitre 10 Mega building was progressing, including roading and infrastructure to service the 8000sq m, $20 million store.
The store is expected to open for business late this year.