Soldiers from the fourth brigade of the Republican Guard were demanding the removal of Abdulmalik al-Arar and another top officer named Abdullah al-Hamiya, the source said, adding that no casualties were reported in the shooting.
The protest follows similar moves by soldiers and police in other areas of the military demanding change since embattled President Ali Abdullah Saleh quit the country last week after handing power to his deputy.
The Republican Guard is led by Saleh’s son, Ahmed, one of several relatives who control Yemen’s main security and military bodies.
On Saturday, hundreds of air force personnel in Sanaa and Taez demanded the ouster of air force commander Mohammed Saleh al-Ahmar, a half-brother of Saleh.
After months of protests, the veteran Saleh finally signed in November a deal under which he agreed to transfer his powers to his deputy Abdrabuh Mansur Hadi.
He also received blanket immunity against prosecution from parliament, as protesters on the streets insisted that he face trial.
Anti-corruption strikes have spread across several military and government departments in the impoverished country where the economy is on the brink of collapse after a year of protests.
Since Saleh took office in 1978, he has carefully chosen members of his regime, appointing relatives to head the military and security apparatus.
In addition to his son and half brother, Saleh’s nephew Yehya commands the central security services and Tariq, another nephew, controls the presidential guard.