Nextgen Networks was organising "wavelength swaps" with other carriers to shore up its fibre services as one of its inter-capital data arteries was severed near Thagoona, west of Ipswich.
"The damaged cable is underwater and expected to be out of service for several days, flood water depending," it said.
Nextgen said that a fault on the other major Sydney-to-Brisbane cable could result in "significant" outages for inter-capital data transmission.
"It should be noted that the network is currently operating unprotected," Nextgen said, referring to the lack of redundant link.
Late this afternoon, that became a reality as the second link went down for approximately 40 minutes.
An issue advisory blamed an electronics fault at Viney Creek, located midway between Sydney and Brisbane.
The outage affected ISPs including Internode.
"All Internode QLD services restored. Network status is back to how it was at 4pm: operational, but vulnerable. Needs a cuddle," Internode network engineer Mark Newton tweeted upon restoration of the link.
Nextgen said it did not expect that controlled environment vaults - electronic regeneration sites on the interstate routes - were in danger of flood damage.
"These have battery back-up for at least two days of operation in the event of a mains power failure," Nextgen said.
"There are also options to mobilise generators to these sites if they were to have an extended power cut which will be access dependent".
Australia's Academic and Research Network (AARNet) told iTnews it suffered the effects of a fibre break near Toowoomba.
ISPs have also reported that they were feeling the effects of fibre cuts on inter-capital routes.
"A fibre break in Toowoomba has required the rerouting of services for the University of Southern Queensland (Toowoomba Campus) via Sydney and services to CSIRO in north western NSW have also been rerouted via Sydney," an AARNet spokesman said.
AARNet also shut a point of presence (PoP) at QUT Gardens Point "on the Brisbane River due to potential flooding and power failures".
"As a contingency measure AARNet had already established an emergency gigabit optical circuit between Sydney and its primary PoP located at the University of Queensland," the operator said.
"This bypasses QUT and the flood-affected fibre to the east. Generally, the back-up circuits are handling the traffic loads well."
The PoP was restored on January 13.
AARNet's spokesman said the organisation was continuing to monitor the situation.
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