That will include businesses in hospitality, gyms, hairdressers and barbers, she said.
The system was designed to bring simplicity to employers.
The EMA is also pleased with the news.
"We have been advocating for simplicity and clarity," said Paul Jarvie, employment relations and safety manager.
Particularly pleasing was the announcement the Government would produce a template for businesses to use in their risk assessments, he said.
This area had been very unclear.
"They'd said: "Just do a risk assessment". I've seen a dozen versions ranging from the ridiculous to great detail. We're happy with it."
Also positive was that staff who did not want to be vaccinated now had some security with the Government introducing a four-week notice period for them.
As always, details had yet to be digested, but the EMA was very supportive of the Government "listening to Business NZ and the CTU".
"It's great to see them working together," said Jarvie.
Workplace Relations Minister Michael Wood said vaccinating was the most important thing Kiwis could do to keep whānau and workplaces safe.
The Cabinet would require vaccinations for all workers where customers must show vaccination certificates to access a business's services, Wood said.
The timing of the new system coming into effect will depend on when Auckland and New Zealand moves into the Government's new traffic light Covid management system.
That could come earlier in Auckland, Ardern said.
In the meantime given there is no exact date for the new traffic light system coming into place, Wood urged workers in these areas to get vaccinated now.
He said employers will have to consult workers and their representatives when making risk assessments about whether their staff need to be vaccinated.
Employers can exempt employees from their vaccination mandates, Wood said.
That can include those who cannot be vaccinated for medical reasons, though that is a very small number of Kiwis, he said.
Wood said the changes will raise questions about what happens when staff refuse to be vaccinated.
He said the new framework will include a minimum new four-week termination process for any employee who loses their job for refusing a vaccination.
The change will only apply to employees who don't have a notice period.
Once the notice period starts the worker will have the four-week period to get vaccinated and show proof of it.
Wood said some employees may find it hard to get vaccinated because they don't have time amid their family commitments.
To help with this, employers will be urged to allow their staff to be vaccinated during work hours and provide other measures to make it as easy as possible.