The commission has asked for its 2015 deadline to be extended by two years, along with an additional $104 million, but is yet to be told the outcome.
Without the extension, the commission says 3000 victims won't be heard.
Commission chairman Peter McClellan reportedly told a closed community meeting in Victoria the uncertainty meant victims may be turned away from September.
More than 2200 abuse victims have had private sessions with the commission, with another 1800 scheduled before the end of the year.
"If the royal commission is not extended, we cannot hold private sessions for any person who contacts us after September or October this year," commission chief executive Philip Reed told News Corp.
A spokesman for Attorney-General George Brandis said the government was "actively considering" the commission's request.
"The government has always supported the important work of the royal commission and has always supported provided sufficient funds for it to carry out its work," he told AAP.
