The Colonial Secretary's Office can be said to have originated with the appointment of Peter Broun as Colonial Secretary on 30 December 1828. However, Broun's letter of appointment of that date from the Colonial Office provides no reference to the duties connected with the office - it was simply intimated to him that he would receive half salary from the date of embarkation and full salary on arrival in the Colony.

The earliest records of the office are copies of letters written by the Colonial Secretary during the voyage, mainly instructions for other members of the Civil Establishment issued under the Lieutenant-Governor's signature, included among them being "Regulations for the Colonial Secretary's Office" dated 16 May 1829. These related chiefly to the internal organisation of the office and the keeping of records. The functions of the Colonial Secretary as the chief administrative office were indicated in the instructions to other officials who were informed "All Applications or Reports to the Governor to be invariably made through the Colonial Secretary's Office".

After Governor Stirling's return from England in 1834, new instructions were issued for the conduct of the official business of the Government. In connection with the Colonial Secretary's Office, it was stated "The main object contemplated in the Establishment of the Colonial Secretary's Office is to conduct the Correspondence of the Governor with the several Departments of the Public Service, and also with Colonists, collectively or individually". Instructions then follow about the regular daily attendance of the Colonial Secretary on the Governor to dispose of business and detailed rules are given for the keeping of records.

How little the Colonial Secretary's Office altered during the years can be seen by comparison of the remarks quoted above with regulations issued forty years later: "In the Colonial Secretary's Office shall be conducted subject to the previous rules, the general correspondence of the Governor with the departments of Government and the public. Subject to the previous rules, the Colonial Secretary shall be the official channel of communication to and from the Governor and the Governor's orders shall be conveyed 'by direction' under his hand".

In addition to the work of his own office, the Colonial Secretary was for two years after the foundation of the Colony required to act as Treasurer, but he was relieved of this responsibility when an Assistant Commissary General was appointed in 1832. From 1834-1839 he was Clerk to the Councils and he acted as Registrar of Deeds until 1846. Also, prior to 1846 when a Colonial Auditor was appointed, a board of three members with the Colonial Secretary as Chairman was responsible for Audit. When other officials took over these various posts, the records directly relating to them were transferred by the Colonial Secretary to the new offices.

The Colonial Secretary was, from the beginning of 1832, a member of both Executive and Legislative Councils. Until the middle 1870's, the Commandant of the Military Forces took precedence over other Council members and presided at Council meetings in the Governor's absence, but after 1873 the Colonial Secretary occupied this position and also, when the Legislative Council became partly elected in 1870, was the leader of the Government in the Legislative Council.

Western Australia ceased to be a Crown Colony in 1890 and on 29 December of that year, the first Ministry under Responsible Government took office, one of the Ministers being the Colonial Secretary. The administrative head of the office from that date was the Under Secretary.

It was not until 1924 that the Minister in charge of this office became known as the Chief Secretary instead of Colonial Secretary, and the title of the office was changed accordingly.

During the years 1890-1900 the Premier, Sir John Forrest, was also at times Colonial Secretary and at these periods the Colonial Secretary's Office files include communications signed by him as Premier.

After Western Australia was granted responsible government the Colonial Secretary was still at the head of an organisation controlling widely diversified affairs such as Customs, Post Offices, Defence, Police, Shipping, Immigration, Education, Aboriginal affairs, Fisheries and many others. These however had the status of sub-departments and kept their own records. Some functions passed to Federal control at later stages, others became departments under their own Ministerial heads. During 1890-1900, work within the Colonial Secretary's Office itself was confined to matters affecting the lives and welfare of the people. It was in fact what might be called the "Home" Department, dealing with hospitals and health, charitable organisations, child welfare, Aboriginal protection, control of newspapers, public holidays, consular matters, etc.

The Colonial Secretaries for Western Australia were:

• Peter Broun (Brown): 30 December 1828 - 1846

• George F. Moore: 1846 - 1847

• Hon. R.R. Madden: 1847 - 1849

• Hon. C.A.J. Piesse: October 1850 - March 1851

• T.N. Yule: March 1851 - 1852 (Acting)

• Fred P. Barlee: July 1855 - July 1875

• Sir Roger T. Goldsworthy: August 1877 - 1880

• Rt. Hon. Baron Gifford, V.C.: September 1880 - 1883

• Sir Malcom Fraser: 1883 - 1890

• Sir George Shenton: December 1890 - October 1892

• Hon. S.H. Parker: October 1892 - December 1894

• Rt. Hon. Sir John Forrest: December 1894 - April 1898

• Hon. George Randell: 28 April 1898 - 27 May 1901

• Frederick Illingworth: 27 May 1901 - 21 November 1901

• Matthew Lewis Moss: 21 November 1901 - 23 December 1901

• Frederick Illingworth: 23 December 1901 - 1 July 1902

• Walter Kingsmill: 1 July 1902 - 10 August 1904

• George Taylor: August 1904 - June 1905 (Acting)

• John Michael Drew: 7 June 1905 - 25 August 1905

• Walter Kingsmill: 25 August 1905 - 7 May 1906

• James Daniel Connolly: 7 May 1906 - 7 October 1907

• John Michael Drew: 7 October 1911 - 27 July 1916

• Hal Pateshall Colebatch: 27 July 1916 - 17 April 1919

• Charles Arthur Hudson: 17 April 1919 - 17 May 1919

• John Scadden: 17 May 1919 - 25 June 1919

• Frank Tyndall Brown: 25 June 1919 - 22 August 1922

• Richard Stanley Sampson: 22 August 1922 - 15 April 1924