While firms expect conditions to improve by September, analysts warned that the pace of Japan's recovery was uncertain amid power shortages following the crisis at the tsunami-ravaged Fukushima Daiichi nuclear plant.
Large manufacturer sentiment in June dropped to "minus 9" from "6" in March, a plunge of 15 points and the first negative reading in five quarters.
The reading was worse than the median forecast of "minus 7" by economists polled by Dow Jones Newswires.
The figure represents the percentage of companies saying business conditions are good minus those saying conditions are bad. The survey is taken into account by the BoJ when formulating monetary policy.
The March disasters devastated entire towns along the northeast coast and left 23,000 dead or missing while wreaking havoc on Japanese industry, pushing the economy into recession in Japan's worst crisis since World War II.
The nation's biggest firms such as Sony and Toyota were forced to shutter plants and halt production due to shortages in electricity and parts after the disaster disrupted supply chains, sending output and exports tumbling.
The June survey showed sentiment among automakers, which were particularly hard hit due to a lack of components, plunged by a record 75 points to "minus 52".
The recent strength of the yen versus other major currencies is also a concern for firms, as it erodes overseas earnings when repatriated.
However, Japan's recovery has been seen to be quicker than expected, as companies approach normal production levels ahead of earlier forecasts amid expectations that reconstruction spending will boost the economy.
The survey showed that big companies expected sentiment to improve to plus two in the next survey in September.
"Business sentiment (among major manufacturers) is continuing to recover gradually, reflecting rebounding production," said Naoki Murakami, chief economist at Monex.
Recent data suggest the worst may be over following the disaster, say analysts. Industrial output posted the second-largest gain on record in May, with a 5.7 per cent on-month rise.
However, the government warned this may have been partly driven by firms boosting production ahead of a government decree to reduce electricity consumption by 15 per cent for three months starting Friday in a bid to avoid blackouts during the peak summer months amid reduced capacity.
"The focus will be on what effect the issue of a power supply shortage is going to have" on the economy, said NLI Research Institute senior economist Taro Saito.
"A V-shaped recovery was tipped as the supply chain has been restored earlier than expected, but it is unclear whether corporate activities will slow down in the July-September period due to power shortages."
Separately, data on Friday showed Japan's core consumer price index rose by 0.6 per cent in May from a year earlier, boosted by surging energy prices and beating market expectations of a 0.5 per cent rise.
The core consumer price index, which excludes volatile food prices, rose for the second consecutive month after gaining in April for the first time in more than two years on higher energy costs.
But analysts expect Japan's CPI to fall back into negative territory in coming months, reflecting an economy mired in deflation as falling prices encourage consumers to hold back on purchases.
Data on Friday showed Japan's unemployment rate fell to 4.5 per cent in May from 4.7 per cent in the previous month, with figures from disaster-hit northeastern Japan excluded, the government said.
Household spending in May fell by an inflation-adjusted 1.9 per cent from a year earlier.
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