Warplanes continued to circle in the skies above Sanaa after the strikes, the witnesses added.
Two air strikes targeted the ministry late on Friday and plumes of smoke could be seen billowing from the building, the rebel media network Al Masirah quoted witnesses as saying.
The alliance said on Monday it had closed all air, land and sea ports in Yemen to stem the alleged flow of arms to the Houthis from Iran after Saudi Arabia intercepted a missile fired towards Riyadh, which it blamed on Tehran.
The Saudi-led military coalition fighting against Yemen's Houthi movement will allow the resumption of global commercial flights to the country, a Yemeni government minister said, easing its nationwide blockade.
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The United Nations, along with dozens of other aid groups, are raising alarm at the blockade imposed on Yemen by the the USA -backed, Saudi-led coalition there, saying Thursday it could lead to "the largest starvation the world has seen for many decades".
The world body has listed Yemen as the world's number one humanitarian crisis, with 17 million people in need of food, of whom seven million are at risk of starvation. "There were two to three strikes on the Ministry of Defense", local journalist Hassain Abukhaiti told RT, confirming that Saudi-led planes are targeting the Yemeni capital.
The Huthis continue to control the capital Sanaa and much of Yemen's north.
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