Authorities say BA.4/BA.5 represented more than 30 per cent of specimens in NSW in the week ending June 18, up from 23 per cent the previous week.
A similar patter has emerged in Queensland, while traces of BA.4/BA.5 in Victoria's metro and regional wastewater have "risen significantly, indicating increasing transmission", according to Chief Health Officer Brett Sutton.
First identified in catchments in April, the variant now accounts for 17 per cent of Victorian infections and is forecast to overtake BA.2 as the state's dominant strain within weeks.
"The department of health anticipates the prevalence of BA.4/BA.5 in Victoria is likely to result in an increase in cases, including reinfections and hospital admissions," Professor Sutton says.
"This is because the strain has a greater ability than BA.2 to evade immunity provided by vaccination and earlier COVID-19 infection."
There is no evidence yet that BA.4/BA.5 is more severe but authorities are "closely monitoring the situation".
While COVID-19 case numbers have been in general decline nationally since mid-April, infections have again begun increasing in some states.
More than 200,000 cases and almost 330 virus-related deaths have been recorded across the country over the past week.
There are currently more than 231,000 active cases Australia-wide - the highest number since June 6 - while more than 3100 patients are in hospital care, a level last reached in mid May.
Victoria reported another 11 COVID-related deaths and 7758 cases on Tuesday, with several state government ministers falling ill following a Cabinet reshuffle.
At least three, including newly appointed Deputy Premier Jacinta Allan, have tested positive since Saturday's caucus meeting, while former police minister Lisa Neville was unable to attend gaving earlier doing so.
Victorian minister Jaala Pulford, who recently recovered from her second bout of COVID, says she can't say whether there has been a "superspreader" event within the party in recent days.
"I would defer to an epidemiologist for an opinion on where people are picking this up," she told reporters.
NSW reported 40 deaths on Tuesday but authorities say they were notified about 26 of them by the Registry of Births Deaths and Marriages and it's likely they occurred before the current reporting period.
In Tasmania, Tuesday's daily case tally of 1228 is its highest since April.
LATEST 24-HOUR COVID-19 DATA:
NSW: 8623 cases, 40 deaths, 1540 in hospital, 49 in ICUs
Victoria: 7758 cases, 11 deaths, 468 in hospital, 35 in ICUs
Tasmania: 1228 cases, no deaths, 45 in hospital, four in ICUs
Queensland: 5268 cases, 19 deaths, 593 in hospital, 14 in ICUs
ACT: 1159 cases, no deaths, 121 in hospital, none in ICUs