Japan has one of the world's oldest populations with many young people deciding that families place too heavy a burden on their lifestyles and careers.
For the whole of 2006, the number of births rose for the first time in six years, leading officials to say a recovering economy was leading to more marriages and children.
But the number of babies born in Japan fell to 546,541 in the six months to June this year, down by 2,714 from the same period in 2006, according to health ministry data released Wednesday.
The number of marriages also fell by 8,040 in the first half of this year, even though Japan's economy has kept expanding and the job market has been improving since last year.
Health ministry officials are scratching their heads.
"The number of marriages fell back after it kept rising until around February. We are having difficulty to think of any direct cause for the latest trend," said Sayuri Narahara, who is in charge of health statistics.
"Speaking on a long term, childbirths are on a decline," she said.
The trend spells a future crisis as a smaller number of workers is asked to support a mass of pensioners. Japan has resisted immigration on any wide scale.
Japan's population shrank by 22,474 people in the six months, a steeper fall than the decrease of 14,827 people recorded in the same term last year.
The fertility rate -- the average number of children a woman has in her lifetime -- had risen to 1.32 in 2006, up 0.06 percentage points from the record low of 1.26 in the previous year.