The rain has caused flooding in some areas, as well as parts of the capital, Apia.
Samoa's meteorological service said the trough was expected to linger for about another two days, the Samoa Observer reported.
SMET technician Emau Toluono said Samoa was experiencing the impacts of a recent convergence of weather systems over the country.
"An active convergence zone which moved from the North previously affected the Islands with moderate to heavy downpours and gusty winds," he said.
Samoa was still at risk of isolated heavy rain for the next two days, "due to the trough's proximity to Samoa".
By Sunday, the high pressure system might strengthen and push the convergence zone and the trough again to the North, providing pleasant weather for the group towards the beginning of the new week.
"And it is not a sign of rain season yet, but it's normally during this transition period that we get some heavy rain in the build-up to the wet season," he said