Factory output grew 3 percent from a year earlier in January, well below the 7.1 percent annual rise forecast in a Reuters poll. Industrial output was up 2.9 percent in December.
Manufacturing output grew by 4.8 percent year-on-year in January, compared with 5.3 percent in the previous month, according to data from the Statistics Department.
The electricity generation sector rose 4.3 percent annually, while mining output grew 1.5 percent, the data showed.
On a monthly basis, factory output fell 4.5 percent.
Malaysia's exports jumped 17.9 percent in January from a year earlier, surging after two months of slower growth, on the back of higher demand for manufactured goods and commodities.
However, a private manufacturing purchasing managers' index showed Malaysian factory activity contracted in February, on a decline in new orders.