"The GCC states will not stand idly by in the face of factional foreign intervention as Yemen's security and the security of the GCC states are one and the same," the ministers said in a statement after talks in the Saudi Arabian city of Jeddah.
Yemeni authorities have accused Iran of backing the Houthi rebels in a similar fashion to their support for Lebanon's powerful Shiite militia Hezbollah.
The GCC ministers "confirm that any threats to the security and safety of Yemen and its citizens is a threat to regional security and stability, and interests of the people."
The rebels advanced from their stronghold in northwestern mountains to the capital Sanaa last month, then seized key state installations with little or no resistance on September 21.
Gulf ministers called the events "regretful" and expressed "their serious concern at the threats faced by the Yemeni government and its institutions."
Under a United Nations-brokered peace deal signed the day the rebels took control of Sanaa, they are supposed to withdraw once a new neutral prime minister is named.
President Abdrabuh Mansur Hadi has so far failed to appoint a new government chief.
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The deal also required Hadi to name an adviser from within the rebel movement.
The Gulf ministers from Bahrain, Oman, United Arab Emirates, Qatar and Saudi Arabia denounced the "armed acts" that occurred.
They called for seized official facilities to be returned to the Yemeni state, and expressed support for United Nations resolutions.
Their declaration came after Prince Saud al-Faisal, foreign minister of regional powerhouse Saudi Arabia, warned over the past week that Yemen risks sliding towards further violence which could damage regional security.
Also known as Ansarullah, the Shiite rebels have battled the government for years, complaining of marginalisation.
The violence has added to instability in Yemen since an uprising that led to the ouster of autocratic president Ali Abdullah Saleh two years ago.
The peace deal aimed to put the post-Saleh transition back on track in impoverished Yemen, a key US ally in the fight against Al-Qaeda.