Acting Commissioner Gavin Freeman told reporters it was still too early to determine what set off alarms within its IT system early on Thursday but did not rule out a hacking attack.
The service was still able to respond to fires but had shut down several internal systems as a precaution.
"Something's breached our systems, not sure what that is at this point," Acting Commissioner Freeman told reporters on Thursday.
"We're certainly delving deep into that, we've got a lot of people working on the investigation to determine it.
"We're not ruling anything in or at this point in time, we need to keep an open mind and conduct our investigation very thoroughly."
Currently, the service's phones, email, website and automated systems are down.
This includes a program that opens station doors as soon as a call-out is received through a computer.
Instead, the Emergency Services Telecommunications Authority (ESTA) is able to send out fire trucks through mobile phones, radios or pagers.
Extra firefighters have been called in to make sure someone is able to listen to radios at all times.
"We've put everything in place to make sure if you call triple zero a fire truck will still come," Acting Commissioner Freeman said.
It's expected the systems will be down for up to four more days, however, and will only be turned back on once authorities were convinced it's safe to do so.
Acting Commissioner Freeman was not aware of any ransomware demands, which occur when malicious software stops companies or users from accessing their own IT systems unless money is handed over.
Cyber security experts for the Victorian and Commonwealth governments are providing assistance.
Premier Daniel Andrews was briefed on the matter earlier on Thursday.
"As I understand it, it is a cyber issue," he told reporters when asked if the service had been hacked.
"But the exact detail of it is not known to me, as I said I had a very broad briefing on it."
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