Infectious disease expert Professor Lindsay Grayson told the inquiry the advice was "inappropriate".
"It's not just about the 1.5 metres (distance), PPE is needed anyway because there is a level of the unpredictability of that 1.5 metres suddenly becoming less in those scenarios," he said.
Prof Grayson said security guards should have been wearing eye protection, gloves, a gown and a mask when interacting with returned travellers or handling objects belonging to them.
The document was shown to the inquiry by Arthur Moses SC, who is representing Unified Security, one of three companies contracted to guard Victoria's quarantine hotels.
Prof Grayson was also shown excerpts from a Commonwealth government training module, which was provided to security guards.
"The majority of it is like a training module for the general public, rather than someone who is going to come into direct contact or be responsible for managing COVID patients," he said.
The module stated people did not need to wear masks to prevent the spread of COVID-19, which was true for the general public at the time but was "misleading for health workers or quarantine staff".
"I would consider it crucial if they were in likely contact with a potentially infectious patient," Prof Grayson said.
The training module was not updated until 25 July.
The head of the Doherty Institute's genomic sequencing unit, Professor Ben Howden, told the inquiry about "99 per cent" of Victoria's second wave of coronavirus can be linked to returned travellers in hotel quarantine.
In late May, when the virus first broke out of hotel quarantine, 19 people in Victoria had died from COVID-19.
The state's death toll now stands at 334, with almost 7500 cases active.
Senior counsel assisting the inquiry Tony Neal QC said the program was set up in 48 hours and was without "precise lines of responsibility, control, supervision and management".
He identified the Department of Health and Human Services, the Department of Jobs, Precincts and Regions as well as Emergency Management Victoria as playing key roles in the program.
But "it was not clear who was in overall command".
"From the beginning, it seems there were multiple and potentially overlapping areas of responsibility between the departments," Mr Neal said.
He said the inquiry would also probe why private security guards were used over the Australian Defence Force and Victoria Police.
Government ministers will be called to give evidence.
Premier Daniel Andrews said he was yet to be called to appear.
"If I am called, I will be there," he told reporters on Monday.
An application by Opposition Leader Michael O'Brien to appear at the hearing, however, was rejected by the inquiry head, retired judge Jennifer Coate.
Mr O'Brien had submitted he had a "direct or special interest" in the probe on behalf of coalition voters, and that his participation would "enable a different voice to be heard".
In her ruling, dated 12 August but posted online on Monday, Justice Coate rejected Mr O'Brien's arguments and defended the independence of her inquiry.
"It will be conducted on behalf of all Victorians," she wrote.
International flights are being diverted away from Victoria while Corrections Victoria has taken over quarantine operations.
The inquiry continues on Tuesday.
Metropolitan Melbourne residents are subject to Stage 4 restrictions and must comply with a curfew between the hours of 8pm and 5am. During the curfew, people in Melbourne can only leave their house for work, and essential health, care or safety reasons.
Between 5am and 8pm, people in Melbourne can leave the home for exercise, to shop for necessary goods and services, for work, for health care, or to care for a sick or elderly relative.
All Victorians must wear a face covering when they leave home, no matter where they live.
People in Australia must stay at least 1.5 metres away from others. Check your state’s restrictions on gathering limits.
If you are experiencing cold or flu symptoms, stay home and arrange a test by calling your doctor or contact the Coronavirus Health Information Hotline on 1800 020 080.
News and information is available in 63 languages at sbs.com.au/coronavirus