Nigeria has the world's seventh-largest natural gas reserves, yet is blighted by persistent electricity outages which force businesses and individuals who can afford them to rely on diesel generators.
"We all know the importance of atomic energy. We have plans to generate power from atomic energy and we must pursue it seriously," Jonathan said at the inauguration ceremony at the presidential villa in the capital.
"We expect you to come up with time-lines for the delivery of atomic energy to our people and we will give you the resources you need to work."
Nuclear power has faced increased opposition in some nations since an earthquake and tsunami damaged Japan's Fukushima nuclear facility in March. Germany, Europe's largest economy, has since announced it will exit atomic power and authorities worldwide have kicked off safety checks on nuclear power plants.
The Nigeria Atomic Energy Commission was established in 1976 to investigate the development of nuclear energy but little progress was made. It was reactivated in 2006 and Jonathan appointed a new team this year.
Critics question why Nigeria needs to spend money on speculative future nuclear projects when vast gas reserves sit untouched under the ground or are flared into the sky.
Despite being Africa's biggest crude oil exporter, decades of corruption and mismanagement mean Nigeria has never built the infrastructure to farm its huge oil and gas resources for much-needed domestic use.
Power shortages are a major brake on growth in sub-Saharan Africa's second-biggest economy, pushing up the cost of business for manufacturers and making Nigeria uncompetitive as an investment destination for industry, despite a population which makes it one of the world's largest untapped frontier markets.
South Africa, with a third of Nigeria's population, has 10 times the generation capacity.
Power shortages also perpetuate social inequality in a country where most of the population survive on $2 a day or less, depriving many of light at night or the ability to power water pumps, let alone recharge mobile phones or access the Internet.