He was employed by Francis Walsingham as an agent between England and Scotland in 1585, and in the following year he accompanied Thomas Randolph to Edinburgh, during the negotiations on the treaty of Berwick.
In 1598, he acted as secretary to Henry Brooke, 11th Baron Cobham, Lord Warden of the Cinque Ports, and in the same year (15 June), he obtained, in reversion after Sir Ralph Bourchier, the keepership of Rochester Castle.
Two years' experience as customer of Sandwich convinced him of the desirability of reviving the staple system, and after consultation with Thomas Fanshawe, remembrancer of the exchequer, he prepared a statement of his views, which was brought to the notice of Lord Burghley.
To meet the attacks made upon the Apology by John Wheeler, secretary to the Merchant Adventurers' Company, Milles published a reply.
His wife died in 1624 at Davington Hall, and was buried by the side of her younger daughter in St. George's Church, Canterbury, where a monument was erected to her memory.