Mr Bodger said the company was "very disappointed and sorry" for the wage deductions taken from employee Kerry McIvor's pay cheque.
"Night n Day chief executive Tony Allison has spoken and apologised to Kerry and we too have called Kerry but are yet to speak with him to apologise. We can confirm that Kerry has been sent reimbursement for his deducted pay," Mr Bodger said.
He was "confident" it would not happen to any other Gull employee in the future, and said "significant steps are being taken to ensure franchisees do not deduct pay from employees for drive offs".
The investigation comes after reports that some petrol stations were docking the wages of attendants if a customer drove off during their shift, charging the employee for the price of the stolen petrol.
Rachel Mackintosh of the Engineering, Printing and Manufacturing Union (EPMU) said that anecdotally "it's pretty common".
The union would regard such docking of wages as illegal, she told TV3's Firstline programme.
"When you sign an agreement you can't have any control over something a third party might do that's not a party to that agreement, so an agreement that purports to give an employer that right is actually not enforceable," she said.
"And if a contract does say that, an employee still has the right to representation in any single case. If an employer wants to recover something because they think the employee has done something wrong and breached their contract, then the employee has a right to representation, has a right to a fair process, not just to have their pay docked."
Many petrol stations attendants were working on their own late at night or through the night and would not feel safe challenging someone who drove off without paying.
"Petrol stations lock their doors so that people can't get in. To expect the petrol station attendant to chase somebody who hasn't paid is completely unreasonable," she said.
Ms Mackintosh advised petrol station workers to join a union, saying the practice of docking wages for drive-offs "doesn't happen" at service stations where workers are organised.
The issue first came to light after reports that staff at a Night 'n Day store in Masterton, which operates a Gull service station, had their wages docked. More petrol station workers have come forward to say they have suffered similar practices.
A spokesperson for Gull told TV3 it was investigating the reports of wage-docking at its petrol stations, saying such a practice was not standard policy.