The $28 billion figure was the midpoint estimate between $15 billion and $38 billion.
It is expected overseas investment would drop by between $4 billion and $7 billion by 2050, while exports could fall by up to $10 billion over the same period.
More than 3000 people would lose their jobs between now and 2050, the report said.
The Petroleum Exploration and Production Association of New Zealand (PEPANZ) – the lobby group who paid for the NZIER study – said the results are "very sobering".
Its chief executive, Cameron Madgwick, said the report showed the need for an independent review and rethink of the Government's policy.
But Energy Minister Megan Woods said NZIER's numbers were based on Ministry of Business, Innovation and Employment (MBIE) figures that she said didn't "accurately model our policy".
MBIE's regulatory impact statement estimated the cost of the ban to be $8 billion between 2027 and 2050.
"I had real concerns the RIS wasn't accurately modelling our policy, and the large amounts of existing permits that will be protected under our policy and available for exploration," Woods said.
MBIE's report only looked at the loss of revenue to the Crown – NZIER's report looks at the impact of the legislation on the New Zealand economy as a whole.
Woods said there would be long-term implications on the environment if nothing had been done.
"That's exactly why we're starting the planning now. This is a long-term, managed transition happening over the next 30 years," Woods said.
National's Energy and Resources spokesman Jonathan Young said the numbers show that New Zealand would be poorer as a result of the ban.
"The ban may read as a step toward a low-carbon economy but this report says its biggest achievement will be to wipe $28 billion off GDP."
Act is also critical, with leader David Seymour saying the Government was "taking a wrecking ball to the economy".
But Greenpeace climate and energy campaigner Amanda Larsson said an oil industry-commissioned report claiming to show the Government's oil and gas exploration ban will cost billions is nothing but "fake news and flatulence".
The NZIER report said that Taranaki would bear the brunt of the ban and predicts unemployment in the regions to increase by between 3.2 per cent and 6.6 per cent.
This is despite the fact the ban would not affect existing permits on onshore exploration in the Taranaki region over the next three years.