The numbers signal continued weakness in trade and dampen hopes of a recovery at the world's busiest container port, after throughput jumped a surprise 19 percent in March from February. Singapore is due to release key non-oil exports data on Monday.
The April fall from a year earlier was steeper than the 14.6 percent decline in March but not as severe as drops of 19.8 percent in February and 19.6 percent in January.
The MPA is responsible for Singapore's maritime affairs, including port operations.
State-owned PSA International , which operates as a commercial company and runs ports around the world, said container volumes at its Singapore port fell 17.6 percent in April from a year ago.
The world trade downturn has battered shipping firms, with Singapore-listed Neptune Orient Lines (NOL) (NEPS.SI) reporting a worse-than-expected $245 million first-quarter loss.
Trade-dependent Singapore saw its deepest ever economic contraction in the first quarter and the government expects the economy could shrink 6-9 percent this year.