Monday's attack hit Al Dabba oil terminal, near the port city of Mukalla in Hadhramaut governorate. The terminal was the target of another assault by the Houthis last month and, on November 9, the rebels struck an oil tanker at Qena port in the Shabwah governorate.
The latest attack was carried out with drones, Yemen's internationally recognised government said, without specifying the extent of damage.
The Houthis said they struck “an oil ship”, without clarifying whether an oil tanker had been hit, or some other vessel carrying fuel.
Houthi fighters have been supplied with thousands of long-range “kamikaze drones” supplied by Iran, as well as short-range ballistic missiles that have enabled the group to strike targets within Yemen and in neighbouring countries.
The rebels have frequently used drones to hit oil infrastructure in Saudi Arabia, although they claim the devices are domestically made and deny getting help from Iran.
Drones have also been used to attack commercial shipping in the Gulf of Aden.
The Houthis appeared to acknowledge Monday's strike, with the group's military spokesman, Yahia Sarea, saying that "the armed forces succeeded in forcing an oil ship — that had come close to the Al Dabba port in the south of the country — to leave".
Yemen's government said the ship was a "commercial vessel".
The country's warring parties failed last month to renew a months-long truce that had spurred hopes for a longer peace.
War has raged since 2014 between the Houthi rebels and pro-government forces backed by a coalition of Gulf Arab states.
The Iran-backed insurgents swept down from the mountains in 2014, occupied northern Yemen and the country’s capital, forcing the government to flee to Saudi Arabia.
Since then, more than 150,000 people have been killed in the violence and three million have been displaced. Two thirds of the population receives food assistance.
The initial, two-month truce agreed to on April 2 was extended twice, until October 2. Since then, both the US and the UN have blamed the Houthis for a breakdown in efforts to extend the ceasefire yet again.
One of the main obstacles to a truce is the use of Yemen’s resources. The Houthis insist that oil produced in Yemen should not be exported by the cash-strapped government.