The Southern Protectorate was established in 1900. It was administered by a High Commissioner. The first High Commissioner for Southern Nigeria Protectorate was Ralph Moor. In 1906, the Lagos Colony was joined with the Southern Protectorate. It, therefore, became the Colony and Protectorate of Southern Nigeria. At this time, the High Commissioner was Walter Egerton.

In terms of administration, the former Lagos Colony became the Western Province while the old Southern Nigerian Protectorate was split into Central Province with capital at Warri and Eastern Province with capital at Calabar. Egerton sent annual pacification patrols in order to force a large part of the South eastern Nigeria that was still outside British control into submission. He approved the extension of the Lagos-Ibadan railway to Oshogbo in 1904. The railway reached Oshogbo in 1907 and was later extended to Zaria and Kano.

By January 1914, the Southern Protectorate became part of the British Nigeria called Southern Provinces. The new administration of Southern Nigeria was divided into three major provinces: Eastern, Central and Western. Each of the major Provinces was governed by a Commissioner. The Provinces were further divided into nine, each of which was under the control of a Resident Officer. It included Benin and Delta Provinces and the Eastern Provinces. The British introduced indirect rule system, which failed in many parts of Southern Nigeria.

Before 1914, the Niger Delta area was governed by a Vice-Consul. The Vice-Consul was assisted by native councils. He appointed chiefs who worked under his supervision and direction. The colonial government made little use of the people’s traditional system of government. This was apparently because of their resistance to the British rule. In the Eastern Provinces, warrant chiefs were appointed in the British bid to enforce the indirect rule system. The warrant chiefs were new men without any connection with traditional political system in the Eastern Provinces. They were supervised by the British political officers. The provinces were divided into districts under the control of District Commissioner who was called the Vice-Consul before 1900. Each local area within a district had a Native Court made of the Warrant Chiefs in the area. The court performed executive, legislative and judicial functions. It was later renamed Native Authority. A British political officer presided over the Native Court. By so doing, the warrant chiefs were merely employees of the colonial government. In Eastern Nigeria, there were riots against the imposition of Warrant Chiefs. The most prominent one was the Aba Women’s Riot of 1929-1930.

In Yorubaland, the British introduced the “Emirate type” of indirect rule system in 1914. Native Authority and Native Courts were established, especially in Oyo under the control of the Alaafin. However, no Yoruba Oba had absolute control of the Native Authority system. They could not collect any direct taxes. There were revolts against the Indirect Rule system in many parts of Yorubaland. For example, the Iseyin rebellion in 1916 was against the imposition of colonial taxes. It was also a protest against the new powers granted to the Alaafin of Oyo by the British colonial government. There were also revolts in Abeokuta and other parts of Egbaland against the Indirect Rule system in 1918. The Alake of Egbaland nearly lost his life in the uprisings.

In the Benin and Delta areas, the indirect rue system was also introduced. As a matter of fact, in Urhobo and Kwale Igbo, warrant chiefs were imposed on the people. This led to riots in various parts of the Delta areas. There were anti-tax riots in Warri between 1927 and 1928. Throughout Southern Nigeria, there were agitations by the educated elites who were excluded from the native administration system by the colonial government. This led to the formation of political parties, pressure groups and newspapers to demand for inclusion in government.