Imports from the US fell 17%, these sorts of as agricultural options and gasoline fuels, the ministry acknowledged.
Exports and imports to different areas, like Europe and China, additionally fell.
The tariff war between the USA and China has taken a toll across Asia, hurting manufacturers and supply chains.
The weaker trade data reflect lower oil prices but also mounting pressure on the economy from a mainstay of growth at a time when consumers are adjusting to an October 1 sales tax hike.
By destination, exports to China, Japan's biggest trading partner, slipped 10.3% year-on-year in October, down for the eighth month as shipments of plastics and vehicle parts declined.
Exports fell 9.2% from a year ago, dropping for an 11th month and extending the longest streak of monthly declines since 2016, Ministry of Finance data showed Wednesday.
Among other partners, Japan's trade surplus with the United States shrank 2.7 percent from a year earlier to ¥557.54 billion amid sluggish auto-related exports.
New data finds that Japan's exports to South Korea have declined sharply amid a South Korean consumer boycott of Japanese goods. The trade balance was a ￥17.3 billion (US$159.61 million) surplus, the first since June.
Analysts said lower export prices exaggerated the decline, but they forecast still weaker demand in coming months.
Exports to Asia, which account for more than half of Japan's overall exports, tumbled 11.2 percent in the year to October, down for the 12th month.
Legislators have called on the government to boost spending by as much as 10 trillion yen ($92.1bn) for the current fiscal year to support the economy, which many fear is facing additional pressure from a sales tax rise that took effect in October.
The nation's overall imports sank 14.8% year-on-year, a smaller decline than the median estimate for a 16.0% decrease.
Private-sector economists said the October 1 increase in the consumption tax appears to have led to a drop in imports, but that it is hard to assess the impact because the natural disasters apparently played a larger part.
A downturn in the high-tech industry, especially for computer chip makers, also is thought to have bottomed out, raising hopes for a recovery in that sector.