The boat is the latest in a string of vessels to attempt the dangerous crossing to Australia`s northwest and news that it was missing came as Australia`s parliament considers new laws to deter boats carrying asylum seekers arriving illegally.
The boat left Indonesia in late June or early July but has not been detected since, Home Affairs Minister Jason Clare told Australian television.
"There is no evidence that those people have arrived in Australia," Clare said, adding Australia held "very great fears" for those missing.
Since 2001, almost 1,000 people have died at sea while attempting to reach Australia on overcrowded and often unseaworthy refugee boats from Indonesia.
In a turnaround for her administration on Monday, Prime Minister Julia Gillard moved to re-open refugee detention centres on the Pacific islands nations of Nauru and Papua New Guinea to deter such arrivals.