The rebuttal on Thursday came a day after the Pentagon claimed that the USS Mason, a guided-missile destroyer, had come under the Yemeni attack for the second time in four days.
"These allegations are unfounded and the army and the Popular Committees have nothing to do with this action," Yemen's Saba news agency quoted an unnamed military official allied with the Houthi movement as saying.
The Pentagon said it hit Yemen's radar sites on Wednesday after the destroyer was targeted by a missile which crashed into the sea before reaching the vessel.
US officials claim the USS Mason and the USS Ponce, an amphibious warfare ship, were previously targeted on Sunday in a failed missile attack from territory in the Red Sea off the coast of Yemen.
The Yemeni official dismissed Pentagon's accusations as an attempt to provide a pretext for the intelligence and logistics support it has provided to Saudi Arabia in its military campaign against Yemen.
“Such claims aim to create false justifications to step up attacks and to cover up for the continuous crimes committed by the Saudi coalition against the Yemeni people,” said the official.
US accusations came in the wake of a Saudi aerial attack on a funeral which killed more than 140 people attending a wake for the father of Yemen's interior minister in the capital Sana'a on Saturday.
The carnage sparked international outcry, drawing attention to military and logistics support provided by the US and its allies to the kingdom and their continued sale of arms to Saudi Arabia.
The US military provides aerial refueling to Saudi bombers carrying out airstrikes in Yemen. Saturday's raid on Sana'a prompted charges of US complicity in the killing of civilians which constitutes an apparent war crime, according to Human Rights Watch.
The carnage also came less than a month after US Senate endorsed a military deal with Saudi Arabia worth $1.15 billion.
Many observers believe US allegations of Yemeni attacks on its warships are aimed at turning away attention from the Sana'a carnage and reducing pressure over its aid to the Saudis.
They say the Yemeni army and its allies are unlikely to have opted for opening a new front, which would only undermine their position in the battle against Saudi Arabia.
The Saudi campaign has killed more than 10,000 Yemenis since its onset in March 2015.
According to a Monday report on the distinguished US-based online publication The Intercept, the United States and Britain are fully aware of the civilian nature of Saudi Arabia’s targets in Yemen and yet continue to provide Riyadh with weapons and intelligence.
London and Washington “have indiscriminately and at times deliberately” led Saudi warplanes to strike civilian targets in Yemen, it said.
On Wednesday, leader of Yemen's Houthi Ansarullah movement Abdul-Malik al-Houthi said the Saudi military aggression against Yemen was being carried out under the supervision of the US.
As he spoke, thousands of people rallied in Sana'a to denounce the Saudi airstrike and accuse the US of complicity.
“We will not give in to the Americans,” chanted the protesters.
“The carnage hit... well-known people from all sides, which has embarrassed the Americans,” Houthi said, Press TV reported.
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