Look at the Equatorial Pacific, Gulf of Alaska, Arctic Ocean: this is what a strong El Niño looks like. pic.twitter.com/swumagsJgP 
— Peter Gleick (@PeterGleick) June 12, 2015 
For Japan this can mean cooler temperatures in early summer:
As a result of El Nino, Japan will experience a cooler than normal summer and a warm winter. Summers will feature cool temperatures and heavy rain, with fewer than normal sunny days. Source. 
Japan experienced its hottest month of May on record, with many regions across Japan reaching temperatures in the mid-30's — temperatures not normally seen before mid-summer.
— 気象予報士 河津真人 (@makotokawazu) May 27, 2015 
I've uploaded the weather forecast – please take a look. “Return of El Nino causes record temperatures across Japan (in May 2015)” – Makoto Kawazu, Meteorologist at TBS Weather Map 
As of mid-June, while the Japan Meteorological Agency is predicting normal temperatures for much of Japan , there should be higher than normal amounts of rainfall for the island of Kyushu  in the southwest. The rest of Japan will probably experience lower than normal amounts of precipitation for June and July.
This is because the El Nino phenomenon is influencing the traditional “rainy season” weather pattern the Japanese archipelago experiences each June and July. The weather pattern, known as tsuyu , or the the baiu zensen, typically begins in late May in Okinawa and the far southwest of Japan.
The rain front gradually travels north from east to west, dousing the entire archipelago in rain in June and early July. The predictability of the rainy season and the progression of the rain front has played a key role in Japanese rice cultivation for more than two thousand years.
This year the baiu rain front has remained stuck over the island of Kyushu in southwest Japan, refusing to budge, hammering the island with heavy rains. Kumamoto and Nagasaki prefectures, located midway up the island have been hit especially hard, with some regions receiving 50 to 80 millimetres of rain every hour.
The steep mountainous terrain of much of Kyushu has turned the runoff from all of this rainfall into raging cataracts that are overflowing onto city streets and causing mudslides. So far more than 30,000 people have been evacuated due to flooding and landslides.
The torrential rains are providing spectacular television footage:
Kumamoto, which lies on the western slope of steep, high hills that are right in the path of rainclouds, is dealing with serious flooding:
— 日刊時事ニュース (@nikkan_jijinews) June 11, 2015 
[The cities of Amakusa and Yashiro are experiencing heavy flooding.] http://t.co/TuXFfBkTio 
Due to an extremely active baiu rain front, a large area of western Japan is experiencing unsettled weather. Kumamoto and Nagasaki prefectures are receiving exceptionally heavy rainfall. – JiJi Nikkan News Service.
Besides the threat of natural disasters such as flooding and devastating landslides, a cooler summer in Japan thanks to El Nino will likely result in poor agricultural production. For Japanese consumers, this means higher prices at the supermarket:
— かも カモ (@c_a_m_o_) June 11, 2015 
It looks like vegetables are going to suddenly cost a whole lot more this summer.
— 詠み人知らず (@yomi_bito) June 7, 2015 
I wonder if our own Rarirureru Lettuce  is going to be affected??? [NOTE: Kagawa Prefecture on the southern island of Shikoku is an agricultural powerhouse  providing high-quality produce throughout Japan.]
- “In Kagawa Prefecture the price of a head of lettuce has tripled since last month. | Kagagawa News | Shikoku Shimbun”
While natural calamities are nothing new in Japan, recent years have seen increasingly wild weather. Last summer torrential rains caused a massive landslide in Hiroshima Prefecture  that killed 74 people in one neighborhood.
広島市の土砂災害で亡くなられた方のご冥福と、早期の復興をお祈りします。 pic.twitter.com/K4dzPDFYa3 
— 美酒乱三世_みちのく一人旅 (@bishuran3rd) August 22, 2014 
We pray that the victims of the  Hiroshima landslides enjoy peace in the next world, and that there will be a quick start to reconstruction.