Between 1841 and 1845, Hampton was surgeon-superintendent on a series of convict ships to Van Diemen's Land: Mexborough, Constant and Sir George Seymour.
Hampton eventually wrote a letter to the Council, in which he agreed to remain under house arrest until the legality of the warrant had been established.
The Council refused to accept this proposal, but a political crisis was averted when the Governor of Tasmania Fox Young appointed a judicial tribunal to pronounce on the legality of the warrant, then prorogued parliament.
While the tribunal was still sitting, Hampton obtained a leave of absence on grounds of ill health, and left the colony.
The final report presented findings that Hampton had engaged in corrupt practices, including the employment of convict labour for personal profit.
He took no government service, spending some of the time in Toronto, Ontario, Canada on "urgent private affairs".
He arrived in the colony the following year, and immediately took far more direct control of Western Australia's convict establishment than had his predecessors.
He imposed a far stricter regime than in the past, with increased use of flogging as a punishment, and the reintroduction of solitary confinement.