Promoted to rear-admiral on 20 January 1858 and appointed Knight Commander of the Order of the Bath (Civil) on 20 December 1858, Milne became Fourth Naval Lord in the second Derby–Disraeli ministry in April 1859.
During his service at the Admiralty from December 1847 to June 1859 he served under four different First Lords of the Admiralty in three Liberal and two Conservative administrations.

Milne became Commander-in-Chief, North America and West Indies Station, hoisting his flag in the second-rate HMS Nile, in January 1860: in this role he acted with diplomacy, especially in response to the Trent Affair on 8 November 1861 during the American Civil War, when USS San Jacinto, commanded by Union Captain Charles Wilkes, intercepted the British mail packet RMS Trent and removed, as contraband of war, two Confederate diplomats, James Mason and John Slidell.
Milne was appointed Knight Commander of the Order of the Bath (Military) on 25 February 1864 and promoted to vice-admiral on 13 April 1865.

Milne became First Naval Lord in the third Derby ministry in July 1866 and in this role took advantage of the Government's focus on spending reduction to ask fundamental questions about naval strategy.
He remained in office until the Derby ministry fell from power 18 months later.

He became Commander-in-Chief, Mediterranean, hoisting his flag in the battleship HMS Lord Warden, in April 1869.
He was promoted to full admiral on 1 April 1870 and advanced to Knight Grand Cross of the Order of the Bath on 20 May 1871. "
In the autumn of 1870 the Mediterranean Squadron, under the command of Sir Alexander Milne joined up with the Channel Squadron for the purpose of carrying out combined manoeuvres off the coast of Portugal, and Sir Alexander, being the senior admiral, took supreme command.
 The low freeboard, fully rigged turret-ship Captain had joined the Channel Squadron a short time before, and the combined fleet put to see from Vigo".
 On 6 September "the fleet was sailing in two columns on the starboard tack in a fresh north-west breeze, and Sir Alexander Milne went on board the Captain in the afternoon to inspect her and see how she behaved at sea, as she was a novelty... During the time the Commander-in-Chief was on board the Captain the wind and sea had increased, and he had great difficulty in getting back to his own ship – the Lord Warden.
In fact, the captain of the Captain (Hugh Burgoyne) tried to persuade him not to risk it, but to remain on board for the night and return in the morning.
Sir Alexander, however, was a dour auld Scotsman and said he would get back to his ship, and did."
That night the Captain capsized and sank and "only the gunner and seventeen men were saved."

He again became First Naval Lord in the first Gladstone ministry in November 1872, remaining in office under the second Disraeli ministry and identifying the critical need for trade protection at times of War and demanding new cruisers to protect British merchant shipping.
He retired from office in September 1876 and was created a baronet on 26 October 1876.

In retirement he was a member of the Royal Commission on the defence of British possessions and commerce abroad.
Promoted to Admiral of the Fleet on 10 June 1881, he lived at Inveresk House in Inveresk where he died from pneumonia on 29 December 1896.
He was buried in Inveresk churchyard on 2 January 1897: the grave lies on the north edge of the original churchyard, near the north-west corner.
Promoted to rear-admiral on 20 January 1858 and appointed Knight Commander of the Order of the Bath (Civil) on 20 December 1858, Milne became Fourth Naval Lord in the second Derby–Disraeli ministry in April 1859. During his service at the Admiralty from December 1847 to June 1859 he served under four different First Lords of the Admiralty in three Liberal and two Conservative administrations.
Milne became Commander-in-Chief, North America and West Indies Station, hoisting his flag in the second-rate HMS Nile, in January 1860: in this role he acted with diplomacy, especially in response to the Trent Affair on 8 November 1861 during the American Civil War, when USS San Jacinto, commanded by Union Captain Charles Wilkes, intercepted the British mail packet RMS Trent and removed, as contraband of war, two Confederate diplomats, James Mason and John Slidell. Milne was appointed Knight Commander of the Order of the Bath (Military) on 25 February 1864 and promoted to vice-admiral on 13 April 1865.
Milne became First Naval Lord in the third Derby ministry in July 1866 and in this role took advantage of the Government's focus on spending reduction to ask fundamental questions about naval strategy. He remained in office until the Derby ministry fell from power 18 months later.
He became Commander-in-Chief, Mediterranean, hoisting his flag in the battleship HMS Lord Warden, in April 1869. He was promoted to full admiral on 1 April 1870 and advanced to Knight Grand Cross of the Order of the Bath on 20 May 1871. "In the autumn of 1870 the Mediterranean Squadron, under the command of Sir Alexander Milne joined up with the Channel Squadron for the purpose of carrying out combined manoeuvres off the coast of Portugal, and Sir Alexander, being the senior admiral, took supreme command.  The low freeboard, fully rigged turret-ship Captain had joined the Channel Squadron a short time before, and the combined fleet put to see from Vigo".  On 6 September "the fleet was sailing in two columns on the starboard tack in a fresh north-west breeze, and Sir Alexander Milne went on board the Captain in the afternoon to inspect her and see how she behaved at sea, as she was a novelty... During the time the Commander-in-Chief was on board the Captain the wind and sea had increased, and he had great difficulty in getting back to his own ship – the Lord Warden. In fact, the captain of the Captain (Hugh Burgoyne) tried to persuade him not to risk it, but to remain on board for the night and return in the morning. Sir Alexander, however, was a dour auld Scotsman and said he would get back to his ship, and did." That night the Captain capsized and sank and "only the gunner and seventeen men were saved."
He again became First Naval Lord in the first Gladstone ministry in November 1872, remaining in office under the second Disraeli ministry and identifying the critical need for trade protection at times of War and demanding new cruisers to protect British merchant shipping. He retired from office in September 1876 and was created a baronet on 26 October 1876.
In retirement he was a member of the Royal Commission on the defence of British possessions and commerce abroad. Promoted to Admiral of the Fleet on 10 June 1881, he lived at Inveresk House in Inveresk where he died from pneumonia on 29 December 1896. He was buried in Inveresk churchyard on 2 January 1897: the grave lies on the north edge of the original churchyard, near the north-west corner.
Sir Alexander Milne, 1st Baronet