Blaine Higgs says many of the agreements date back to the early 1990s when the tax often wasn't collected at all.
He says many agreements can outlive their intended use and he wants to determine if there is an unfair advantage that is making it difficult for competing businesses.
Kevin Lacey, the Atlantic director of the Canadian Taxpayers Federation, says the agreements allow aboriginal retail businesses to remit just five per cent of the provincial tax they collect on gas sold to non-aboriginals.
He says that gives those businesses an advantage over their non-aboriginal competitors.
Lacey wants the agreements cancelled, but Higgs says that would not help find a solution to the problem.