The month-on-month rise compared with economists' median estimate of a 0.9 percent increase in a Reuters poll, and followed a 2.8 percent drop in April, the Ministry of Economy, Trade and Industry data showed.
Manufacturers surveyed by the ministry expect output to fall 0.7 percent in June and increase 1.5 percent in July, the data showed.
The ministry maintained its assessment of factory output, saying it is in a flat trend.