Fistfights broke out at some polling booths in the north where ballot papers had failed to materialise. Ink to show a person had voted was not indelible.
After casting his ballot in Yaounde, the capital, Biya said: "What I expect right now is a comfortable majority, which will enable me to build and modernise the country."
The RDPC, which has been in power for decades, currently holds 149 seats in the assembly. Two opposition parties hold 27 seats and the rest are held by parties allied to the ruling party. Biya's party also holds 290 of the nation's 336 mayoral seats.
A representative of the opposition Social Democratic Front (SDF) said the authorities had distributed electoral cards that had not been collected by residents and had paid people to vote.
Jacob Beide, co-ordinator for a group of election observers from African non-governmental organisations, said: "Fraud attempts and fraud have been reported - at least one case of ballot box stuffing and the majority of people are voting without identity cards."
Five million of the country's 16 million people were eligible to cast their votes, but turnout appeared to be low.
John Fru Ndi, leader of the SDF, said: "The organisation of the elections has not changed. It has even worsened. The elections will be unfair and won't be transparent. And Biya is the architect."
Biya was appointed prime minister in 1975 and has been president since 1982.
Graft is rampant in the country which is regularly listed as among Africa's most corrupt by Transparency International. Biya is accused of trampling on democracy and human rights. Wealth from oil industry has not reached the millions of poor.
Official results are expected within two weeks.