US President Barack Obama has declared an  emergency in the states of New York and Pennsylvania  after heavy rains flooded much of the US northeast, killing at least five people.

The formal declarations authorize federal agencies to coordinate disaster relief efforts in order to "save lives and to protect property and public health and safety," the White House said in a statement.

Heavy rain yesterday swamped areas of the US northeast already sodden from Hurricane Irene, with up to five people killed as flash floods forced over 100,000 to leave their homes.

The National Weather Service (NWS) issued a flash flood warning for counties in New York, New Jersey, Pennsylvania, Connecticut, Maryland and Virginia, as towns became inundated, busy highways closed down and commuter lines backed up.

The latest foul weather is the remains of Tropical Storm Lee, which slammed into the Gulf Coast on Sunday, dumping torrential rains on a huge swath of the American south, mid-Atlantic region and heavily populated northeast.