He said pregnant staff would be unable to climb to safety.
After the union rang Burger King head office the padlock was removed with the company stating it was a misunderstanding, he said.
But last month Hastings management had again padlocked the fire exit gate and told staff to "Jump the gate - this is no longer a fire exit".
The union sent an email to Burger King Head Office, stating that a fence that has to be climbed is not a fire escape and that employees have the right to withdraw from work if health and safety is compromised.
The company replied saying the issue had been addressed.
"After this experience it is distressing to find that the same thing has been happening at Burger King Napier for years."
Yesterday the union lodged complaints with the labour division of the Ministry of Business, Innovation and Employment and the fire service.
Burger King marketing director Rachael Allison said it would not happen again and welcomed government inspections.
"On each of the occasions that we learned the gate has been locked, action was taken straight away to have the lock removed," she said.
"We take extremely seriously our duty of care to staff and those visiting the restaurant.
"The gate is positioned between the restaurant's general service yard and an open public carpark area at the rear of the building. Our investigation revealed that the gate had been locked to increase the security of staff and the restaurant following separate security incidents at two different restaurants in November 2011 and July this year. Unfortunately, the lock which was taken off in February, was put on again in July."
She said there may have been times when the Napier service yard was locked to protect the property of staff members following theft, but that was no longer the case.
"These actions were taken by different managers who genuinely believed there were serious security concerns and there were sufficient other escape routes (three).
"We do not agree, and it has now been made absolutely clear that all emergency exits in all of our restaurants including Hastings must be unlocked and unimpeded at all times.
"While the union might be publicly critical of the historic actions of managers to enhance the security of the restaurant and its staff in furthering its current campaign against Burger King, we can understand their actions in locking the gate, although do not condone them."