The surprise move rattled stock market investors, with the Nikkei 225 index swinging between gains and losses after the announcement. It closed 2.8% higher.
The Japanese yen slid, with the US dollar rising to about 120.70 yen from about 118.50 earlier in the day.
The central bank said it is imposing a 0.1% fee on some new commercial bank deposits with the BOJ, effectively a negative interest rate. It hopes it will encourage commercial banks to lend more, rather than keeping cash at the BOJ, and stimulate investment and growth in the world's third-largest economy.
The BOJ said Japan's economy is still recovering, but risks from volatile global financial markets could undermine confidence and slow progress towards the central bank's 2% inflation target.
Bank deposits with the BOJ will be divided into three tiers. Existing current account balances will earn a 0.1% positive interest rate.
Required reserves held at the central bank by financial institutions will earn zero interest. Any additional current account deposits would incur the minus 0.1% rate, the BOJ said.
The bank "will cut the interest rate further into negative territory if judged as necessary", it said.
It said the policy would continue as long as needed to achieve its inflation target. In the meantime, the BOJ pushed back its timeframe for achieving that goal from late 2016 to mid-2017.
"We think there is an increasing risk that an improvement in the business confidence of Japanese firms and the conversion of deflationary mindset may be delayed, and that the underlying trend in prices might be negatively affected," BOJ governor Haruhiko Kuroda said.
The European Central Bank has already imposed negative interest rates, after leaving interest rates near zero failed to entice banks into seeking higher returns through lending.
In Japan, keeping interest rates near zero has likewise failed to yield the desired results, raising doubts about the credibility of the quantitative and qualitative monetary easing policies announced by Mr Kuroda in April 2013.
Data on Friday showed Japan's core inflation rate for 2015, excluding volatile food prices, at 0.5%.
That and other figures show the economy remained anaemic last year as stagnant incomes, the slowdown in China and the mixed blessing of lower oil prices hobbled prime minister Shinzo Abe's recovery strategy.
Consumer spending fell 4.4% in December from a year earlier, as households chose to save rather than splurge on any gains from the low oil prices that are slowing inflation. It was the fourth straight month of year-on-year declines.
Industrial output fell 1.6% in December from a year earlier, partly due to slower demand for machinery and electronics components and devices in China.
Mr Abe took office three years ago vowing to get growth back on track through massive injections of cash by the government and central bank, and by sweeping reforms to boost competitiveness.
The central bank said it would also persist with its "quantitative easing" purchases of about 80 trillion yen (£463 billion) of government bonds a year.
The aim is to end a long spell of deflation, or falling prices, that is thought to be discouraging corporate investment.
But while corporate profits have soared as massive stimulus weakened the Japanese currency, making earnings made abroad worth more when converted into yen, investment and wages have lagged.
Average incomes fell 2.9% from a year earlier in December. Even though unemployment was steady at 3.3% and the job market remained tight, companies wary over the economic outlook are opting not to raise pay.