Deputy Prime Minister Prawit Wongsuwon took sick leave on Wednesday and missed the first cabinet meeting chaired by Prime Minister Prayut Chan-o-cha following his return to Government House.
The Constitutional Court ruled that Prayut could carry on serving as prime minister, potentially until 2025 should he win next year's general election.
Prawit's absence on Wednesday followed rumours that he was offended by remarks made by the premier on Monday during a teleconference call about the flood situation.
Prayut was quoted as telling the meeting that he did not want to see any welcoming committees.
"I'm healthy and can take care of myself. Please take care of people in need of assistance. I'm not a burden," Prayut was quoted as saying.
A spokesman of Prawit said the deputy prime minister, who made visits to several central provinces on Monday, fell ill with fever.
He tested negative for Covid-19.
Following the cabinet meeting, Prayut said he would pay a visit to Prawit at his house, but refused to respond when asked if Prawit was sulking in response to his comments.