It is criticised for being a predominantly Ovambo party. South Africa, playing on tribal rivalries, denounced SWAPO as an Ovambo force.

SWAPO was accused of human rights violations against its own cadres. Following South Africa's successful attacks on SWAPO bases in Angola and Mozambique, SWAPO arrested, detained and tortured some of its cadres on allegations of spying for South Africa.

The organisation has also been blamed for changing the Constitution to secure a third term for Sam Nujoma. There are fears that that act began a process to sustain the organisation and its leadership in power forever.

SWAPO also began to recruit members from rival political organisations such as SWANU and the Democratic Turhalle Alliance (DTA). This brought it into conflict with other political parties, hence derailing the struggle for independence and democracy after independence.