The Index pared back some losses in the afternoon session, closing down 0.2 percent at 12,877, which meant it had exited bear market territory for the moment.
The market was driven lower by a resurgence in the yen late Thursday—which strengthened to as much as 95.96 against the U.S. dollar. A stronger yen is typically negative for the Japanese market which has a heavy concentration of exporter stocks.
Disappointment over Prime Minister Shinzo Abe's longer-term growth strategy known as the "third arrow" of his three-pronged approach to turning around the economy has also been a drag on the market - which fell almost 4 percent on Wednesday after Abe delivered his plan.
(Read More: Japan Fires 'Third Arrow', but Will It Work?)
Abe announced that he would be setting up special economic zones and pledged to raise incomes by 3 percent annually over the next decade, but economists told CNBC that the success of the plan, which comes after monetary and fiscal stimulus, would depend on proper implementation.
Rogers, who is bullish on the stock market over the long-term forecasting it could double from current levels over the next 2-4 years says it's "way too premature" to say "Abenomics" is going to fail: "That's the kind of conclusion people are trying to draw at the moment," he said.
Ben Collett, head of Asian equities at Sunrise Brokers in Hong Kong, said he wouldn't recommend reentering the market until a clearer base is formed.
"When you get a 20 percent down move in a market, people get more confidence about the bear case in Japan," Colette said.
"You need to let the market find a support. If we find stability around 12,500, traders and investors will put money to work. What you don't do right now is start running into this and start filling up the truck," he added.
(Read More: Why Japan Equities Sold Off on Abe's Plans)
Where to Next for Nikkei 225?
With volatility plaguing global financial markets, strategists say it is unclear where equities are headed next, with Friday's U.S. non-farm payrolls data a key risk event.
The U.S. economy created 175,000 new jobs in May, slightly above expectations and strong enough for Federal Reserve officials to continue their talk of tapering of bond purchases.
Dhiren Sarin, technical analyst at Barclays, said that while he remains upbeat on the Nikkei in the medium-term, he expects the market to trade in a large range of 12,000-14,500 in the coming weeks.
(Read More: Market Strife Puts Japan Policies in a Flux)
A slew of economic indicators are also released out of Japan next week. These include first quarter gross domestic product estimates and current account data on Monday with a two-day Bank of Japan (BOJ) policy meeting concluding on Tuesday - all these will be crucial in determining the market's next move.
"The BOJ press conference on Tuesday will be crucial considering the big moves we've seen in the yen and Nikkei. Officials will want to steady the ship - they may say something that's a game changer," said Stan Shamu, market strategist at trading firm IG Markets.