Wind speeds dropped to around 40 mph (65 kph) and the storm appeared to be breaking up, forecasters said, and it could be downgraded to a tropical wave in the coming hours.
The system still brought large amounts of rain that caused flooding that damaged hundreds of homes in Haiti. The hurricane center warned that the threat of flooding and mudslides remained as the system headed toward Cuba and the Bahamas.
The government ordered the evacuation of more than 5,000 people in the Dominican Republic because of the potential for flooding from heavy rain. The country closed its courts, congress and many other government offices. Aviation officials said more than a score of flights to and from the two countries were canceled.
Emily dropped more than 5 inches (140 millimeters) around the southwestern Dominican city of Barahona and an equal amount was still expected in the area, said Miguel Campusano, a forecaster with the Dominican meteorology office.
In Haiti, about 600,000 people are still in flimsy tents and shanties because of the January 2010 earthquake, strong winds whipped through palm trees in the capital while heavier rains fell further north, damaging homes as well as a cholera treatment center, said Marie Alta Jean-Baptiste, the country's civil defense director. But there were no reports of deaths.
In the capital, which has most of those left homeless by the earthquake, the rain was relatively light so far, but the government evacuated a few families from a camp for quake victims to a school that is being used as a storm shelter, said Jean-Joseph Edgard, an administrator in Haiti's Civil Protection Department.
About a hundred people were staying in temporary shelters in the southern beach town of Jacmel and 25 inmates from a jail in the coastal town of Mirogoane were taken to a nearby police station, said Emmanuelle Schneider, a spokeswoman for the U.N. Office for the Coordination for Humanitarian Affairs.
Schneider said the UN mission also sent heavy equipment to the Central Plateau to help repair a road cut by floods. A team of sanitation specialists also traveled to the area to help stem the flow of cholera after a treatment center for the waterborne disease flooded.
The storm seemed to pause Thursday morning, then resumed a slow march to the west-northwest off the coast of the island Haiti shares with the Dominican Republic, and forecasters said they expected it to hit Haiti later in the day. Emily earlier had maximum sustained winds of 50 mph (85 kph).
John Cangialosi, a hurricane specialist with the hurricane center, said up to 20 inches of rain was possible in isolated high-elevation areas. That is enough to cause serious problems in a country prone to catastrophic flooding.
There was reason for concern. A slow-moving storm in June triggered mudslides and floods in Haiti and killed at least 28 people. Widespread poverty makes it difficult for people to take even the most basic precautions.
Joceline Alcide stashed her two children' birth certificates and school papers in little plastic bags that aid groups handed out. It was her only means to protect herself.
"There really isn't much more we can do. We just got these bags," the 39-year-old Alcide said, standing outside her teepee-like tarp shelter.
The National Hurricane Center said the storm was moving to the west-northwest at about 10 mph (16 kph) and it was centered about 60 miles (100 kilometers) south-southwest of Port-au-Prince.
Based on reporting by The Associated Press.