The shareholder alleged that BHP had not complied with the mine’s joint venture agreements and therefore sought intervention from the Ontario Superior Court of Justice.
Mining major BHP had earlier signed an agreement in November 2012 to sell its stake in the mine.
The lawsuit additionally includes other minority stakeholders, Dr Stewart Blusson and Archon Minerals, though they do not intend to oppose the sale.
Fipco has sought for the sale to be terminated and a directive to BHP to provide the company with a revised offer.
Both BHP and Harry Winston have refuted the claims, calling them without any merit.
Harry Winston released a statement that said, "The Company and BHP Billiton believe that the claim by Fipco is entirely without merit, and intend to vigorously defend the action in order to proceed with the purchase and sale of the Ekati Mine."
If the dispute is ruled in favor of BHP Billiton and Harry Winston, the transaction is expected to be completed by 15 May 2013.