The weather bureau said lower-than-average rainfall has been caused by an El Nino, a weather pattern arising from the warming of the sea surface over the equatorial areas of the Pacific Ocean.
The phenomenon hits countries in the Pacific basin once every few years, sometimes with deadly results.
"A weak El Nino is currently taking place," the bureau said in an advisory.
"The expected deficit in rainfall will have adverse impacts on agriculture, water resources, hydropower generation, health and sanitation, and other sectors."
It said the weather pattern was expected to prevail "through the next five to six months."
Rainfall levels have been below average in the northern half of the main island of Luzon since early September, when the southwest monsoon season ended earlier than usual, and the movement of tropical cyclones were displaced northward, the bureau said.
The bureau predicted below normal rainfall conditions will also hit much of the central islands and the western half of the southern island of Mindanao, the country's bread basket, in the first three months of 2005.
Agriculture accounts for about one-fifth of the country's economic output but employs nearly half the Filipino workforce.
Farm output grew at a 4-year high of 6.82 percent in the nine months to September.
Agricultural output plunged sharply in 1998 following the El Nino weather phenomenon the previous year.