Gross domestic product shrunk by 2.3% during the period from a year earlier, much worse than 1.4% contraction that analysts had forecast.
Compared with the previous three months, the economy shrank by 0.6%.
The numbers are a big blow to Japan’s efforts to recover from the earthquake and tsunami last year.
“The economy is slowing down by more than what was expected,” Martin Schulz of Fujitsu Research Institute told the BBC.
“The slowdown of exports is taking a heavy toll on industry.”
The data comes amid concerns of a slowdown in the global economy, not least due to the ongoing debt crisis in the eurozone.
The crisis has hurt confidence and dented consumer demand in Europe, which is a key market for Japanese goods.
Meanwhile the high rate of unemployment in the US, the world’s largest economy, continues to be a concern despite encouraging economic data in recent weeks.
Exports have fallen a lot because of a triple shock from Europe, the strong yen and floods in Thailand”
At the same time, some of Asia’s biggest economies such as China and India have also started to show signs of slowing growth.
To make matters worse, Japanese companies have had to deal with a strong yen. The Japanese currency has risen more than 7% against the US dollar since April last year.