The final Markit/Nikkei manufacturing Purchasing Managers' Index (PMI) for Japan rose to 48.2 in April from 48.0 in March, up from the preliminary reading of 48.0. It was the lowest level since January 2013.
March's figure was revised down from 49.1.
A reading above 50 indicates expansion, a reading below 50 indicates contraction of activity.
Output, new orders and input prices declined at a faster pace in April.
"Latest survey data signalled a marked deterioration in operating conditions at Japanese manufacturers, partly a consequence of the two earthquakes which struck one of Japan's key manufacturing regions," economist at Markit, Amy Brownbill, said.