Power was cut across much of the center of the island as well as nearby Leyte province - including Tacloban city, which was so badly devastated by Hurricane Haiyan last year.
"We can expect that heavy rains were dumped on Eastern Samar because Ruby hovered for a long time over the coastal areas," weather forecaster Jori Loiz said on radio.
The storm was said to be moving at a relatively slow speed of 16 kilometers per hour (10 mph). PAGASA said Hagupit - the name of which means "lash" in Filipino - was headed on a path northwest towards Masbate, Romblon and Oriental Mindoro provinces, slightly north of the areas badly flattened by Haiyan.
"Ruby's lashing will be severe," Interior Secretary Manuel Roxas told government radio. "Let's be alert. Let's evacuate to prevent any harm to your families."
The country's national disaster agency said residents of low-lying villages and landslide-prone areas had moved to schools, civic centres, town halls and other public buildings. However, the relief agency Refugees International said in a statement that it was "deeply concerned" that evacuation centers may not be safe.
The United Nations Office for Disaster Risk Reduction (UNISDR) in Geneva said about a million people had fled their homes by the time the hurricane made landfall.
"Typhoon Hagupit is triggering one of the largest evacuations we have ever seen in peacetime," said UNISDR spokesman Denis McClean.
Forecasters warned the hurricane could cause storm surges as high as five meters, and would also bring heavy rains to the capital Manila, although it would not hit the city directly.
