The struggling team, who emerged from the remains of the failed Marussia outfit after going into administration and missing the last three races of 2014, failed to turn a wheel on the track in Melbourne.
They missed all three practice sessions and Saturday qualifying, blaming software problems, which ruled them out of the race.
However, they escaped sanction with stewards deciding to take no action after an enquiry decided the team had made "all reasonable endeavours" to get the cars ready.
"We should have never ever, ever allowed Manor to do what they’ve done. It’s our fault. I predicted this would happen," Ecclestone told Reuters.
"They had no intention of racing in Australia. Zero. They couldn’t have raced if someone had gone there with a machine gun and put it to their head.
"It was impossible. So they had no intention. We’ll have to see now. And they will have to pay their way to get there and get out of there," he added.
Marussia, who were ninth overall last season thanks to a ninth-place finish by Frenchman Jules Bianchi in Monaco, won a race against time to get their cars through crash tests and onto the air charter for Australia.
Ecclestone said there had been no charge for the freight because they were entitled to that providing they were competing.
"They are not competing so they have to pay for that," he added.
The team are in line for some $50 million of revenues from last season but would have forfeited the right to that if they had not turned up to compete in Australia with cars that satisfied the regulations.
"We knew we had the possibility of unknown problems and we haven’t had the benefit of sorting some of those problems out in pre-season testing," sporting director Graeme Lowdon told Sky Sports TV on Saturday.
"But equally we had to come here on the basis that we’re racing so we brought all of our normal equipment. There’s 28 tonnes of equipment to support these cars and all of the staff.
"We are trying very hard but it is a tough thing to do in the time available."
(Editing by Tony Jimenez)
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