Flooding forced the closure of the Panama Canal on Wednesday for the first time in 21 years and heavy rains were being blamed for at least two deaths.
More than a thousand people were also evacuated because of what authorities called historic flooding.
"We're taking measures to normalize transit operations in the coming hours," Manuel Benitez, the executive vice president of canal operations, said on Wednesday afternoon.
The last time the canal closed was on Dec 20 1989, when US troops invaded the country to topple president Manuel Noriega.
The country's Civil Protection System declared that eastern Panama was on high alert and issued evacuation orders for about 1,500 people in dozens of flooded neighborhoods.
Authorities recovered the bodies of two girls who were on a boat that capsized in the town of Chepo in the southeast part of the country.
About 5% of the world's naval commerce moves through the canal, and the US is its main user.