According to the Cabinet Office, the orders declined 3.7 percent in May from a month earlier.
Excluding those for ships and utilities because of their volatility, the orders totaled 907.9 billion yen (8.2 billion U.S. dollars) in the recording period.
The latest reading from the Cabinet Office comes on the back of a 10.1 percent increase in April.
Machinery orders are a key advance indicator for corporate capital spending and the government uses the data to predict the strength of business spending in a six to nine month period ahead.
Such business investment accounts for roughly 15 percent of Japan's gross domestic product GDP).
Types of machinery included in the monthly government survey comprise engines and turbines, heavy electrical machinery, electronic and communication equipment, industrial machinery, machine tools, railway rolling stock, road vehicles, aircraft, ships, water crafts, as well as sub types in these categories.