President Abdrabuh Mansur Hadi was not at the palace located in the capital Sanaa when suspected al-Qaeda gunmen attacked a checkpoint outside the compound manned by guards, killing five of them and capturing others, a security source told AFP.
An exchange of fire broke out and went on for more than 20 minutes, according to other security sources and witnesses, amid reports that three of the assailants were killed.
Also today, Yemen's defence minister, Mohamed Nasser Ahmad, and two senior security officers escaped unharmed when al-Qaeda militants ambushed their convoy as they returned from a tour of the south where the army is battling the jihadists.
The army launched a major offensive on April 29 against al-Qaeda in the Arabian Peninsula (AQAP) strongholds in three provinces, two in the south and one in the centre, and claims it has inflicted heavy losses on the jihadists.
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Sanaa has been on alert for days and tensions rose after the army announced troops had entered Azzan, a jihadist bastion in southern Shabwa province, prompting the closure of the US embassy on Thursday.
That night security forces killed al-Qaeda commander Shayef Mohammed Said al-Shabwani, one of the jihadist network's most wanted leaders suspected of masterminding the abduction of Western diplomats.
Authorities say al-Qaeda commanders were among dozens of jihadists killed since the army launched its offensive 11 days ago in the south, where US drone strikes this year have killed scores.
AQAP is regarded by Washington as al-Qaeda's most dangerous franchise and has been linked to failed terror plots in the United States.
On Monday the interior ministry warned that "huge losses" in jihadist ranks "will push al-Qaeda to commit hysterical and desperate acts."