“We learnt overnight that the vessel was double booked and that the Australian charter was not on it," said a Department of Foreign Affairs spokesman, adding the Government had received a firm booking from the charter company.
"This has happened frequently over the last few days, not just to Australia but to a number of other governments."
The Government is hopeful it can get the 350 people queuing at Beirut’s main port onto ships from other friendly nations such Britain, the United States, France and Canada.
It says it has firm bookings to evacuate 2,400 more Australians by Sunday, with secured vessels booked to evacuate 800 people each day on Friday, Saturday and Sunday.
Speaking during a visit to the port, Australia’s ambassador to Lebanon Lyndall Sachs promised ‘a dedicated ship’ would arrive on Thursday.
Earlier in the day, the trapped Australians were terrified when two bombs exploded just one kilometre away
"There was just two bombs, they just bombed twice very close by to us," Australian Angela Zene Hadchite told Sky News.
"I can see smoke ... but I don't know what direction it came from. The floor just shook beneath us."
Mrs Hadchite said she believed the bombs were from an Israeli aircraft and described the scene in Beirut as chaotic and unbearable.
"I'm not used to seeing dead bodies, and bombing and hearing the kids scared.
"There's no clean drinking water, there's a limited supply of
fresh fruit and vegetables."
Around 200 Australians have already been bussed to Syria to escape bombing raids launched by Israel last week after the militant group Hezbollah kidnapped two of its soldiers.
More than 7,000 Australians are registered with the embassy in Lebanon.
Canberra has said there 25,000 Australian citizens living in Lebanon, although the vast majority had dual nationality and did not plan to leave.
Members of Australia's Lebanese community have criticised the government’s evacuation effort.
Rockdale town mayor Shaoquett Moselmane said the Government had shown no urgency.
"It could only be described as shameful in the full meaning in the word," he said.
Others complained it was impossible to access the Internet to read government bulletins, and questioned why Australia was not broadcasting advice on Lebanese television as other countries were doing.