Canberra security contractor Certis is in a dispute with the union representing security workers union over pay on January 23, the day the airport was forced to close under threat of fire.
While the union says some workers had their pay docked, Certis says that is not true.
"One employee chose not to attend work despite having an alternative travel route available. It was suggested to the employee to take a paid day of annual leave, which the employee chose not to do and did not turn up for their shift," a Certis Security AU spokesperson said. "A second employee left Canberra Airport to check on their property, and then returned to work. This employee will be paid as normal."
But the union said three union members were affected, with non-union workers also likely to have been affected. They had "mixed" employment status, a spokeswoman said.
On January 30, Certis's aviation security manager at the airport emailed staff saying those who "failed to turn up for their shift" on the day were entitled to leave without pay, but she was going "above and beyond" to also offer the option of paid annual leave.
The union spokeswoman said Certis had still been paid by Canberra Airport, so should pay its workers as normal.
United Workers Union spokesperson for Property Services Damien Davie said, "To dock workers' pay because they have needed time to protect their homes and ensure the safety of their loved ones is absolutely shameful.
"United Workers Union had highlighted SNP Security, when it was a local family-run business, as an industry leader. This has changed dramatically since SNP was absorbed into Certis."
The Certis spokesperson said the union's allegations were unfounded.
"Certis Security Australia is committed to working with our employees to reach practical solutions when faced with challenging circumstances such as the recent bush fires," the company said.
Head of Aviation at the airport Michael Thomson said, "We have reached out to Certis Security today but will not make a comment on an issue between a contractor, their staff and the union."