Otto was moving west near 9 miles per hour and the hurricane center said it could re-emerge over the Pacific as a tropical storm, the Associated Press reported.
A massive natural disaster of magnitude 7.0 has hit offshore El Salvador, following which a Tsunami alert was issued.
There is a danger of mudslides and flooding in parts of Costa Rica and Nicaragua, Weather.com added.
In La Cruz, residents in the mainly tourist area of Bahia Salinas are bracing for strong winds and heavy rains.
Hurricane Otto made landfall as a risky Category 2 hurricane on a sparsely populated stretch of Caribbean coast in Nicaragua today, becoming the southernmost hurricane on record to hit Central America.
This NOAA-NASA GOES Project image obtained November 24, 2016, shows Hurricane Otto over Central America.
Otto is the first storm to make the jump from Atlantic to Pacific in 20 years.
Heavy rains from the rare late-season storm have been blamed for three deaths in Panama.
At least nine people have been killed in Costa Rica in the wake of Hurricane Otto, the government said on Friday.
"All protection mechanisms have been activated under which we have started evacuations", the minister in charge of the emergency response, Aristides Valencia, said on state radio.
The country's National Meteorological Institute noted that a hurricane had never made landfall in Costa Rica since record-keeping began.
A police official, Luis Guillermo Fonseca, said two of the storm´s victims died in villages close to the Nicaraguan border and the other two in Bagaces, a village north of the capital San Jose.
Bernardo Reina said he'd been stocking up on supplies and would be hunkering down when the storm hit.
A fierce hurricane and a powerful offshore natural disaster struck Central America at the same time Thursday, triggering emergency responses in Nicaragua, El Salvador and Costa Rica, and prayers among fearful populations.
The early effects of Hurricane Otto killed at least three people and left five more missing in Panama before tracking into Nicaragua.
More than 4,000 people have been evacuated from the storm's path in Costa Rica and 10,000 in Nicaragua.
"Otto is the southernmost landfalling hurricane in Central America on record", the USA hurricane centre said.
While Otto is expected to reach the Pacific coast later on Friday, it is feared coffee crops, that are nearly ready to be picked, could be badly damaged in the storm.