The average strength of the garrison was 2,719. On 19 May 1843, Lt Gen Sir Patrick Stuart was appointed Governor and Commander-in-Chief in and over the island of Malta and its dependencies.
In 1842, the Long Wards of the General hospital was vacated by the lessee and handed over to the Ordnance Department.
The new prison on Corradino Hill was completed in 1843.
On 6 Mar 1843, Pte John Naylon 88th Regiment, was on sentry duty at the Dockyard, when for no apparent reason shot and killed Dr William Martin, Deputy Inspector at the Naval Hospital. On 14 Apr, Naylon was acquitted of murder on the grounds of monomania, but was sentenced to the galleys for life with labour in the public works with a chain.
Naylon was an Irish labourer from Castlereagh. He enlisted on 4 Apr 1831, and became non effective from the 88th Regiment at Malta on 4 Apr 1843. His records state that he was transported for the period of his natural life on 2 Apr 1843, but he served his sentence in Malta, where he was reported to have died in a mad house.
He was eventually returned to England. Naylon had no next of kin. Pte Patrick Quigley 88th Foot, who was was unrelated to him, was nominated by Naylon as his next of kin.
On 2 Feb 1843, the Protestant burial ground was extended on the glacis, in the north entrenchment of the Msida Bastion.
On 22 Apr 1843, the quarantine of vessels and passengers arriving from the Ionian Islands, with the exception of those arriving from Athens or Syria, was completely abolished. Merchant vessels arriving from Greece which had a certificate from Her Britannic Majesty's Consul showing that there was no disease in the country, had their quarantine reduced to 7 days, and were no longer required to unload their cargo.
Quarantine imposed on vessels and cargoes arriving from Egypt was not reduced, but that inflicted on passengers was reduced from 20 to 16 days. The quarantine imposed on vessels, passengers, and goods arriving from Turkey was left unaltered.
As soon as the above notification was received at Malta, passengers and vessels from Corfu were set free. Men who were doomed to one day more of quarantine than their wives, having arrived on different vessels, had the delight of joining hands, when a moment before a wooden bar was opposed to the display of attachment. Others, homeward bound, were at liberty to go via Marseilles, whereas before they had no other choice than via Gibraltar.