The latest toll from emergency services and local authorities said at least 60 people died in storms fed by torrential downpours that hit the provinces of Hadramaut and Mahara on Thursday and Friday.
But the toll could rise further as rescue teams searched for victims who may still be trapped in homes swept by the floods and as the authorities launched an airlift to fly aid to the stricken areas.
A first batch of six aircraft took off from the capital Sanaa on Saturday loaded with tents, food and medicine for the Hadramaut capital Al-Mukalla and Mahara, airport officials said.
"Other airlifts are scheduled for later in the day," an official said, adding that public and private organisations had joined ranks to help victims of the disaster.
Yemeni President Ali Abdullah Saleh toured Al-Mukalla on Friday to oversee operations after tasking a government commission with handling the rescue effort.
The authorities said six people had been killed by lightning in the southern provinces of Tayez and Lahj, and a mother and son also died when struck by lightning in the Al-Mahwit region north of Sanaa.
Rescue coordinators said that among the victims were seven people who perished in Al-Mukalla, which is on the shores of the Arabian Sea.
Both Hadramaut and Mahra provinces have been officially declared disaster zones.
Bad weather continued to batter southeast coastal regions on Saturday.
On Friday military helicopters and others operated by oil firms were hampered by strong winds as they fought to rescue thousands of people stranded by the floods, according to one emergency official.
Local authorities in Yemen said that more than 500 houses were destroyed across Hadramaut province and 3,500 families were made homeless. Flooding also caused heavy damage to roads and power and water networks.
The United Arab Emirates has said it will send emergency aid.
An official said that among the affected areas was the UNESCO world heritage site of Shibam which was totally cut off by the flood waters and where historic buildings were threatened with collapse.
Shibam, with more than 20,000 residents, is famed for its high-rise mudbrick buildings, mostly dating from the 16th century, that have given the town the moniker "the Manhattan of the desert."
It was established in the third century and built with the profits from frankincense, which is still sold there.
Floods and lightning also claimed the lives of at least 25 people in April 2006 across eight provinces of the impoverished Arabian Peninsula country.