He is listed as surgeon of H.M.S. Buffalo in a dispatch by Governor King dated May 1803. 
In 1804 H.M.S. Buffalo conveyed those involved in establishing the settlement at George Town, Tasmania under William Paterson. The surgeon appointed to the expedition was Jacob Mountgarret, however John MacMillan probably served as assistant surgeon on the Buffalo on this expedition. A burn (stream) was named McMillan stream although later changed to Massey's Creek. 
A supply of vaccine lymph, obtained from the Royal Jennerian Society, was despatched to Surgeon Thomas Jamison in the transport ship Coromandel, which arrived in May 1804. A second packet of lymph also arrived on the same vessel, addressed to assistant surgeon John Savage, which was ‘put up in a different way from that sent by the Royal Jennerian Society’. On receipt of the lymph, Dr Jamison immediately successfully vaccinated three children at the ‘orphan asylum’ and some other persons were vaccinated by Mr Savage. 
John MacMillan successfully vaccinated several children and others on a voyage from Norfolk Island to Hobart late in 1805 using vaccine he had obtained from surgeon D'arcy Wentworth at Norfolk Island before returning to Sydney late in 1805 bringing the vaccine with him.
An incident recorded in the Sydney Gazette places John MacMillan in Sydney in February 1806 when he attempted to save the life of a young lad -
On the afternoon of Thursday 23d ult. the youngest son of Wm. Wall was taken lifeless out of a hole of water in the stream leading to the tanks between Serjt. Major's and Pitt's Row ; all the resident Medical Gentlemen immediately attended, and adopted the mode prescribed by the Humane Society with an earnestness that reflects honor to their feelings but unhappily without success. Mr. MacMillan Surgeon of His Majesty's ship Buffalo, assisted in the general endeavour to produce resuscitation, and continued his labours until a late hour, but respiration was irrecoverably lost.
John MacMillan was still in Sydney when William Bligh took over as Governor of the colony in August 1806 however planned to depart on the Buffalo soon afterwards.
In an advertisement in the Sydney Gazette in September 1806 Macmillan was asking for claims to be presented (John Oxley, Master of the Buffalo, Mr.MacMillan, surgeon and J. Sherrard, purser), however the Buffalo was still in the colony in December 1806 when an inquiry into the conduct of Daniel Lye and Joseph Swabey Tetley took place. For an account of the inquiry see Copy of the proceedings of a first court of inquiry, with opinion of Philip Gidley King into complaints of 1st Lieutenant Joseph Swabey Tetley and the Master Daniel Lye against 2nd Captain Joseph Short, 10 - 12 December 1806.
John MacMillan signed a memorial to Governor Bligh dated 14 December 1806 regarding the health of Daniel Lye. The memorial has been digitised by - State Library NSW and can be viewed online -
Pursuant to an Order from His Excellency William Bligh Esquire, Captain General and Governor in Chief in and over His Majesties Territory of New South Wales and its dependencies, Captain of His Majesty's Ship Porpoise and Senor Officer of His Majesty's Ships and Vessels employed within the said limits etc
We have repaired on board His Majesty's Ship Porpoise and there taken a strict and careful Survey on Mr. Lye whom we found confined to a small cabin that is ill ventilated and so small as not to admit him to use sufficient exercise for the preservation of his health. Altho' it is not very materially impaired at present still we are of opinion that a continuation of the confinement in this climate under these circumstances must eventually prove injurious to health and in all human probability in time induce disease of the most serious and fatal tendency.
Given under our hand at Sydney in New South Wales this 14 day of December 1806 (signed)
John Harris, Surgeon, NSW Army Corps;
J. MacMillan, Surgeon, HMS Buffalo.
Copy of a letter received by Governor William Bligh:
Dated 14 December 1806 
News of the affair reached England in 1807 where it was noted in the Naval Chronicle that Captain Short, late commander of his Majesty's ship Porpoise, had been tried by a Court Martial, on charges of drunkenness, cruelty and oppression, to Mr. Daniel Lye, formerly of that ship. The charges were not proved, and he was consequently acquitted. 
Departure of the Buffalo
The Buffalo departed Port Jackson with Governor King and family on 10 February 1807 bound for England.
They were given a grand send off
At 2 o'clock on Sunday afternoon His Excellency the late Governor and Family finally embarked on board His Majesty's ship Buffalo for England, accompanied to the Wharf by His Excellency, who expressed the most sensible regret at taking leave. His Honor the Lieutenant governor and many Officers attended also to share in the last duties of respect. At half past two the boat left the wharf, and was saluted by His Majesty's ship Porpoise as she passed; the following morning His Excellency's dispatches were on board, and on Tuesday the ship sailed. Governor King designing to touch at Norfolk Island on his way. - Sydney Gazette 15 February 1807
The voyage was long and tedious and took nine months to complete. They called at Rio de Janeiro on 24th May where they refitted the vessel, departing Rio on 20th August. However the voyage was slow because of a damaged hull. The Buffalo arrived safely back in England in November 1807. 
John MacMillan was appointed Surgeon to the Navy on 5th December 1807. He was appointed to the position of Surgeon on the Buffalo at Portsmouth in 1807.
Surgeon Superintendent Speke 1808
Macmillan was employed as Surgeon on the convict ship Speke to New South Wales in 1808. The Speke departed England on 18th May 1808 and arrived in Port Jackson on 15th November 1808
In Australia he joined H.M.S. Porpoise in place of Edward Luttrell
The history of H.M.S. Porpoise can be found at Wikipedia - H.M.S Porpoise was the former mercantile quarter-decked sloop Lord Melville, which the Royal Navy purchased in 1804 to use as a store-ship. She sailed to the colony of New South Wales in January 1806. She was the flagship of William Bligh when he was governor of New South Wales and played a prominent role in the Rum Rebellion. In May 1810 Porpoise sailed from Sydney; after arriving in Britain she underwent a major refit. After voyages to the West Indies, the Cape of Good Hope and North America she served as a harbour ship at Woolwich and Sheerness. She was laid up in 1814 and sold in January 1816. She then returned to mercantile service under her original name (Lord Melville) and made one voyage transporting convicts to New South Wales, and a second to Van Diemen's Land (in 1818).'
When H.M.S. Porpoise under command of ex-Governor Bligh departed Australia on 12 May 1810 she was accompanied by H.M.S. Hindostan and H.M.S. Dromedary, carrying the officers and soldiers of the 102nd. Regiment of Foot (NSW Corps) who had been relieved of their command by the 73rd Regiment, 
Surgeon Superintendent Lord Melville 1818
John Macmillan was Surgeon on the Lord Melville to Van Diemen's Land in 1818.
He was on the navy list of surgeons unfit for duty in 1847
John Macmillan, Esq., M.D., died in Perth, Scotland in 1859.
He entered the Royal Navy and became full Surgeon in 1807. He was for some time on the South Sea station, and after his return to England became, in 1820, a Fellow of the Linnean Society. He subsequently retired to Culross in the county of Perth, where he died on the 1st of the present month, after a long illness, at the age of 81.