"We are saddled with the painful, but important task of completing the implementation of the International Court of Justice's judgment by handing the Bakassi peninsula to Cameroon," Aondoakaa said at the ceremony.
A Cameroon government official said the finalisation of the transfer marks "the end of a crisis", which Cameroon believes began in December 1993 when the Nigerian army occupied a number of villages on the peninsula.
Political disagreements, a last-minute lawsuit and occasional gun battles had stalled the transfer, already staggered over two years.
The transfer has been described by Ban Ki-moon, the UN secretary-general, as "a model for negotiated settlements of border disputes".
But around 90 per cent of the population in the Bakassi peninsula, estimated at 200,000 to 300,000, are thought to be Nigerian fishermen and their families.
Many have said that they do not want to become Cameroonians. Nigeria has offered to resettle them, though critics say that process has not been adequately examined.
Bassey Ewa-Henshaw, a senator for Cross Rivers South state, to which Bakassi used to be a part, told Al Jazeera that the transfer could lead to conflict in the future.
"Our main concern has been the people - the people have never been consulted. In the 21st century where the UN guarantees all kinds of people's rights, adequate preparations have not been made for their relocation," he said.
"One of our greatest worries has been the fact that we are creating a large population of very disgruntled people - and in the last few weeks and months there have been a number of skirmishes organised by Niger Delta militants with the co-operation of the people in the area."
Cameroon first took its case for sovereignty over the Bakassi peninsula to the ICJ in The Hague in 1994.
After a drawn-out legal battle, the ICJ ruled in 2002 that the peninsula should be given to Cameroon, basing its decision largely on a 1913 treaty between Britain and Germany, the former colonial powers.
Cameroon and Nigeria then signed an accord, known as the Green Tree agreement, in New York in 2006 during US-facilitated mediation talks, paving the way for Nigeria's withdrawal from Bakassi.