Convict Ship Hibernia arrived in Hobart on 11 May 1819. The voyage had not been a happy one for one of the passengers on board - Rev Richard Hill. The voyage had taken 172 days and for most of that time there remained between Charles Carter and Rev. Hill a high degree of acrimony.
In correspondence to the Governor on his arrival in the colony Rev Hill complained of the treatment he had received during the voyage. He resented being refused permission to visit the sick in hospital and was offended by Carter's attitude towards him during the voyage. He accused Carter of allowing prisoners to tear up bibles to use as playing cards and of not forcing the prisoners to attend Divine Service.
Charles Carter replied in a lengthy correspondence - Rev. Hill has fully merited the treatment he has received from me and my contempt of his conduct throughout, from his constant extreme officiousness in every duty of my office together with his very insulting manner towards me on various occasions which had it not been for his sacred profession I should have resented in a way it deserved.
Charles Carter thought that nothing tended to depress the spirits of the sick more than such untimely visits as Rev. Hill proposed making! He admitted that he never suppressed card playing as he believed that during a long voyage the minds of most men required now and then the solace of some light amusement, however he denied allowing the prisoners to tear up bibles to make the cards. He sent off his own letters of complaint regarding Rev. Hill to Lord Bathurst  There were three deaths of convicts on this voyage.
Charles Carter was next appointed to the Hebe convict ship which departed England 31 July 1820 and arrived in Sydney on the 31st December 1820. One convict died on the passage out.
His next appointment was to the Arab which arrived in Hobart on 6th November 1822. Charles Carter was later thanked by the Governor for establishing a school on board the Arab under the direction of W.A. Brett and using articles that had been provided by Lady Grey before leaving England.  Four deaths occurred on the voyage.
Sir Godfrey Webster 1823
The Sir Godfrey Webster departed England 1 September 1823 and arrived in Hobart 30 December 1823 with 180 male prisoners under the care of Charles Carter. There were no deaths on this voyage. No deaths on this voyage
Henry Porcher 1825
His last appointment as Surgeon Superintendent on a convict ship was to the Henry Porcher which arrived in Sydney on 3 December 1825.
The following correspondence in the Historical Records of Australia explains in part how it came to be that this was the last voyage Charles Carter made as surgeon superintendent on a convict ship -
Governor Darling to Earl Bathurst.
Despatch No. 4, per ship Triton; acknowledged by Earl Bathurst, 12th July, 1826.
My Lord, New South Wales,
4th February, 1826.
I have the honor to transmit to Your Lordship the accompanying Letter, which was addressed to me on my arrival by Archdeacon Scott, with three Enclosures, respecting a mis-understanding which took place on board the Henry Porcher, Convict ship, between the Revd. Mr. Kean, a Passenger, and Mr. Carter, the superintending surgeon. The case was in fact disposed of before my arrival, as far as it could be here, Mr. Carter having refused to appear before a Court of Enquiry, which the Lieut. Governor had ordered to investigate the facts stated by Mr. Kean. I have since seen Mr. Carter, who contends that, having delivered over the Convicts, placed under his charge, in good order, he has fulfilled his duty; and that he is not amenable, to an investigation for his conduct towards a Passenger.
Without entering into the merits of the present question, it would appear that Mr. Carter s conduct has not been wholly unexceptionable on other occasions; as the accompanying Paper, which has been delivered to me by the Archdeacon, relates to a misunderstanding between him and the Revd. Mr. Hill who is a most zealous and respectable man, when coming- out to the Colony some years since. I am extremely sorry to trouble your Lordship on this occasion, and should not have done so, could the matter have been otherwise disposed of. I beg to submit that the best means of preventing a recurrence would be to direct that Mr. Carter may not return to this country in the convict service. I have only to add that I have furnished Mr. Carter with the usual Certificate of his having delivered over the Convicts in good order, and I have signified my intention in the Certificate to make this report to your Lordship, in order that the Commissioners of the Navy may be duly apprized of Mr. Carter s proceedings. I have, etc, Ra. Darling
Charles Carter was appointed to the Malabar in 1836 .
Emigrant ship Palmyra
Charles Carter was appointed Surgeon Superintendent on the emigrant ship Palmyra, which arrived on 26 September 1838. Many of his patients on this voyages were babies and children. There were cases of scarlatina, bronchitis and hydrocephalus and he regretted that he could not employ adequate means of treating them. This seems to be his last employment as surgeon superintendent. He was on the List of Surgeons remunerated for services as Surgeon Superintendents and was paid £200 for his employment on the Palmyra.
The Medical journal of the Palmyra, emigrant ship from 11 May to 9 October 1838 by Charles Carter, surgeon and superintendent, during which time the ship was employed in conveying emigrants to Sydney - available at National Archives
Later Naval Service
In 1840-42 he was appointed Surgeon to H.M.S. Calcutta in the Mediterranean . H.M.S. Calcutta was built in 1831 and of 2299 tons. 435 officers and men, 60 boys and 150 marines were on board. Sir Samuel Roberts, C.B. was Captain and George K Wilson Commander. James M. Deas M.D., and M.J. Dill, M.D. were employed as Assistant Surgeons 
In 1845 Charles Carter was appointed to H.M.S. Terrible .