AURIZON vice president Scott Riedel looks forward to seeing the back of "iconic flaws" in the company's enterprise agreements.
Without them, he thinks Aurizon will be able to operate more efficiently.
"The current EA (enterprise agreement) had no forced redundancy," Mr Riedel said.
"But work goes up and down, and we need (employee numbers) to go up and down as well."
Aurizon won the right to terminate a number of employee enterprise agreements from the Fair Work Commission on April 22.
At a Resource Industry Network briefing on Friday, Mr Riedel said giving Aurizon the right to make workers redundant was an "iconic flaw" from the original enterprise agreements the April ruling would see rectified.
The new agreement will come into effect from May 18, and while Mr Riedel said there would be a drop in pay and forced redundancies for some workers, he indicated there was no reason to panic.
"We could have said 'all conditions are out', but we want to reach an agreement with our people," he said.
"It was more important for us to get the flexibility that comes (with the new agreement)."
The Fair Work Commission decision saw coal train workers strike on Wednesday, but Mackay workplace consultant Craig Joy agreed the ruling would make Aurizon more efficient.
"I don't think employees will be so perturbed by it," he said.
"They have generously said they are going to maintain redundancy entitlements.
"(Although) they haven't worked out the details yet."
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