The refund relates to qualifying expenditure by Mercator in the year ended 30 June 2018.
The subsidiary is entitled to apply for another refund in the current year (to 30 June 2019), which it estimates will be around A$370,000 (£198,000), although there is no guarantee of this.
Included within last year’s tax return, Mercator has carried forward corporate income tax losses of A$66.2mln (£35.5mln) in respect of historical losses which are available to carry forward.
“I am pleased to confirm the receipt of a significant cash refund by MGA our Australian subsidiary,” said chief executive Craig Brown.
“This incoming cash augments existing cash resources and will applied toward the company’s active gold exploration programmes in Australia.”
ECR shares rose 22% to 1.04p on Tuesday afternoon.