"A total of 28 Huthis (Shiite rebels) and 20 of our men were killed in the fighting, which continued into the evening," General Misfer al-Harithi, who commands the army's 19th Infantry Battalion, told AFP.
Earlier, Harithi gave a death toll of 28 rebels and 14 soldiers.
He said the clashes erupted when rebels and allied forces loyal to former president Ali Abdullah Saleh attacked government positions in Bayhan district on the border between Shabwa and Marib provinces.
"Our forces managed to recapture several positions," Harithi said.
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"We will not stop fighting until we take control of the entire sector," he added.
The area where the fighting is taking place is the only part of Shabwa province still controlled by the Iran-backed rebels.
Forces loyal to President Abedrabbo Mansour Hadi, backed by the firepower of the Saudi-led coalition, managed to drive rebels out of Shabwa and four other southern provinces in the summer.
Today's fighting flared despite an early April ceasefire that paved the way for ongoing peace talks in Kuwait.