Since the end of the military rule in 1999, human rights defenders (HRD) have been able to work in a more favourable environment. However, this is only true for mainstream organisations working in major urban areas. Defenders working on certain human rights issues or in certain regions of the country continue to face serious challenges.

In particular, in the Niger Delta, the heavy militarisation significantly affects the work of human rights defenders, and there are frequent instances of attacks, intimidation and killings of defenders and protesters. The military and the police are in many cases involved in human rights violations against the population, including extrajudicial killings and violent dispersal of protesters. The work of defenders in monitoring and denouncing violations by the military and the police makes them a target of retaliation and violence. Defenders intervening in such cases have been arbitrarily arrested and on several occasions have had their documents confiscated.

Women human rights defenders (WHRD) face serious challenges especially in certain specific areas of the country including the Northern states, where Sharia law is applied, the South-East and South-West, where traditional practices and customs are stronger. The work of women defenders in those areas focuses primarily on such issues as polygamy, child marriage, inheritance and female genital mutilation. Religious groups and traditional communities often distrust organisations working on women's rights. Name calling, verbal assaults, physical attacks and sexual harassment have been reported as the main violations against WHRDs.

Defenders working on discrimination against lesbian, gay, bisexual and transgender (LGBT) people face specific risks throughout the country and often fear for their security. LGBT rights defenders have been under attack and there is no legislation or protection accorded to HRDs that advocate for the rights of these minorities. Hostility by society at large is fostered by the attitudes of State institutions and is reflected in legislation. Homosexuality is criminal under the Sodomy Law, which is used to target LGBT rights defenders. In 2006, the government tabled before parliament a bill prohibiting advocacy around issues of discrimination on the basis of sexual orientation and gender identity and restricting freedom of association for LGBT rights defenders.

Corruption and good governance are sensitive issues and there have been instances of defenders and journalists reporting on those issues being targeted and harassed. Civil servants working on such issues face risks as well.

Despite legislative improvements, the legislative framework remains insufficient to ensure adequate protection to the work of human rights defenders. The police in Nigeria have used the Public Law and Order Act to disrupt public gatherings and muzzle human rights defenders and political activists. The Supreme Court of Nigeria declared the Public Law and Order Act unconstitutional, yet the Parliament has not amended the Act and the police continue to implement it. There is no law guaranteeing freedom of information. In 2004, a bill guaranteeing access to information was passed by the House of Representatives but was then vetoed by the President on national security grounds.