The health and labor ministry said the disaster, which left nearly 20,000 dead or missing, was mainly behind a decline in average lifespan by 0.4 years to 85.90 years. That put Japanese women behind Hong Kong, in the top spot with 86.7 years.
The ministry said a rise in the number of suicides last year also contributed to the decline.
For men, average life expectancy fell 0.11 years to 79.44, leaving them tied for 7th place with Italians. Switzerland led male longevity rankings with average expectancy of 80.2 years.
As a result of advances in health care and falling birth rates, Japan, the world's 10th most populous nation, has become one of the world's oldest and fastest ageing societies.
The trend has been particularly pronounced in the northeast, where, even before the March 11 earthquake and tsunami, scarcity of jobs had been driving young people away. Many of the victims of the disaster were elderly residents who stayed behind.