The Suburban Rail Loop Authority asked the state's remuneration tribunal to sign off on pay increases for three taxpayer-funded roles on the mega project.
The 26km eastern section of the loop, which will run from Cheltenham to Box Hill, is expected to open in 2035 and estimated to cost up to $34.5 billion.
Packages for the director of tunnelling and the director of operations were lifted to $465,000 and $428,831 respectively, above the maximum standard of $401,017.
A third request to raise the salary of the project's executive general manager of land planning, environment and sustainability higher than $533,431 was refused.
Assistant Treasurer Danny Pearson asked the tribunal to look at the salaries the executives before he became transport infrastructure and SRL minister in October 2023.
"I want to make sure that we're paying fair value," he told reporters at state parliament on Wednesday.
"These projects are incredibly complex and we've got to get the best and brightest in the field."
Ambulance Victoria and Victoria Police - both government agencies - remain locked in protracted pay negotiations with their workforces.
Paramedics have been scrawling messages on ambulances since March as part of industrial action, while police union members last week voted down a deal for a 16 per cent pay rise over four years and a staggered move to a nine-day working fortnight.
Asked if it was fair to be handing up salary top-ups to rail loop executives when paramedics and police were fighting for better pay, Premier Jacinta Allan shifted responsibility for the decisions to the tribunal.
"There are independent processes that those salaries go through," she said.
Opposition finance spokeswoman Jess Wilson pointed out Victoria's net debt was on track to hit $187.8 billion by mid-2028 as the public sector wage bill balloons.
"The Allan Labor government must justify why time and again, taxpayers are paying over the odds for executives to run some of Victoria's most blown out, delayed and poorly managed projects and agencies," she said.