Nine countries from around the region, as well as Australia and New Zealand, are in Tonga to sign the PACER Plus agreement, wrapping up nearly a decade of negotiations.
The deal has been polarising with critics saying it threatens the interests of island countries, and was unbalanced towards the interests of Australia and New Zealand.
But proponents tout it as a new kind of deal that links development to trade.
Todd McClay said this would give funding to boost exports from Pacific countries, and create rules to make it easier for the region's countries to trade.
"It's a high quality agreement that gives certainty to exporters but really will help the Pacific Island countries meet some of the requirements of international trade," he said.
"What that really means is they can transform and modernise their economies, they can look at trade-related infrastructure, they can meet the requirements and rules that trading nations of the world now demand."
He also adds he was not worried by the refusal of three of the Pacific's largest economies to sign a regional free trade agreement.
Fiji, Papua New Guinea and Vanuatu would not be there, as they're refusing to sign the deal for various reasons, including that it's unbalanced towards the two metropolitan countries.
Mr McClay, said he was not worried by the refusal, and PACER Plus would always be a flexible work in progress.
"I'm quite relaxed about them not being ready to come on board at the moment. After all, this is not about forcing peoples' hand."
"It's about partnership and they will see over time the benefits of the agreement, and for any country that's not ready the door remains open for them to sign when they are."