The country has made up a good portion of the energy gap by burning liquefied natural gas (LNG), and also coal and fuel oil. While LNG emits less CO2 than coal, it is still a significant emitter (the nuclear value chain, including mining and fuel processing, has a very small CO2 footprint, as do solar and wind). On top of that, the country imports its fossil fuels from far afield - Japan has precious little of its own coal, oil or natural gas. That incurs extra environmental demerits through the high CO2 emissions of overseas shipping.
"A permanent shutdown (of Japan's nuclear) would boost annual CO2 emission by 60 million tons - or more than 5 percent - as the nation draws extra power from burning fossil fuels, according to the country's Institute of Energy Economics," writes New Scientist, in a kindred story to NPR's.
There's a similar CO2 rise in Germany, which began phasing out nuclear power and using more coal after the events at Fukushima. Germany has closed 8 nuclear plants, and plans to shut its remaining 9 by 2022.
"The additional German emissions alone could add up to more than 300 million tons by 2020, which according to the World Nuclear Association, would 'virtually cancel out the 335-million-ton savings intended to be achieved in the entire European Union by the 2011 Energy Efficiency Directive'," New Scientist notes.
Both Germany and Japan have significant plans to use solar and wind energy. Germany is already one of the world's largest generators of solar electricity (the largest by many measures, although some rankings now put Italy on top). But solar and wind generally cannot provide the steady "baseload" power that nuclear can.
The country has reasons other than environmental to continue to seek energy efficiency gains. The fossil fuel imports are subject to geopolitical instabilities, as the LNG comes largely from the Persian Gulf, threatened by tensions in Iran.
The imports have even flipped the manufacturing powerhouse's long vaunted trade surplus. As the NPR article notes, "The country now spends more on imports than it earns from exports. What is Japan buying? Fuel." It sites figures from the International Energy Agency in Paris pegging Japan's daily fuel import bill at $100 million. One IEA analyst says that Japan would use 20 percent of the world's supply of LNG if it kept going at its current rate.
And let's not forget why Japan built up its nuclear energy profile in the first place. As the CIA handbook points out, the country "has virtually no energy natural resources." It is "the world's largest importer of coal and liquefied natural gas, as well as the second largest importer of oil," the CIA says. That's a dubious distinction in an era of globally intense political and industrial hydrocarbon volatility.
Nuclear power, and its CO2 avoidance, could well rise up the international environmental agenda, especially as post-Fukushima time goes by. Just yesterday, word leaked that the UK government wants the European Commission to include nuclear as a "renewable" source of energy in 2030 targets for the European Union.