However, he said, it was usually employees at smaller businesses who had trouble with the clause.
"It's not the big businesses who had trouble because they have good recruitment processes," Popata said.
He said the union tried to encourage employers to use probationary periods instead as 90-day trial periods were "draconian".
"Your recruitment process should be good enough you don't need the 90 days," he said.
"For those who want 90-day clauses, we've been able to talk through the benefits of having a proper probation clause."
Federated Farmers Rotorua-Taupo president Alan Wills was happy the trial period would remain for small businesses, which encompassed most of the rural sector.
"I think it's worked pretty well because employees understand it and there's plenty of protocols around it," Wills said.
"The recruitment doesn't get everything right and you can't expect it to. Some things may turn up that take you by surprise. These 90 days is an opportunity to try to resolve any issues."
Wills said he had never used the 90-day trial period to end an employment and didn't know many employers who had, but it was good to have if needed.
E Tu union national secretary Bill Newson said the changes were improvements.
"We see this bill as a big leap forward towards a fair and equitable society."
However, the union was disappointed that 90-day trial periods could remain for employers with 20 or fewer workers.
"There isn't a majority in Parliament in support of scrapping the 90-day 'fire at will' law in its entirety, which is disappointing," Newson said.
"This is the nature of a coalition government under MMP. It's now our task, as part of the wider labour movement, to improve this part of the bill."
Workplace Relations Minister Iain Lees-Galloway said the bill aimed to lift union numbers and wages.
"For the last 30 years, working people have received a diminishing share of economic growth, and we're trying to restore some balance," Lees-Galloway said.
Other changes would guarantee workers rest breaks, allow them to engage in low-level industrial action and give union workers the right to the same conditions as workers on a collective agreement.
The bill, to amend the Employment Relations Act, will be introduced on Monday, and will have its first reading in February.
Under the new law, a worker will:
• have guaranteed rest and meal breaks
• engage in low-level industrial action without the threat of pay deductions
• have the right to the same conditions as other workers on a collective agreement, if you're a new worker
• have guaranteed pay and conditions, if you're a vulnerable worker and your employer changes.
