The incident occurred at about 2.30pm at a security checkpoint at the Administrative Reception near a clinic, located on the premises.
The operative was said to be trying to empty the weapon before submitting it at the security point when the bullet went off.
The operative and the female worker, who was also making her way into the premises at the time, were injured in the process.
The woman, who sustained injuries on her abdomen, back and thigh, was quickly taken to the clinic for first aid treatment.
She was thereafter driven to the State House Medical Centre in Asokoro for further medical attention.
She was said to be in a stable condition at the time of filing this report.
That was the second time such an incident would happen in the Presidential Villa in the last one year.
On February 23, 2016, a security operative, attached to the delegation of the Danish Foreign Affairs Minister, Mr. Kristian Jensen, who visited Vice-President Yemi Osinbajo, was said to have attempted to pass through the last security checkpoint with his weapon.
Based on the rules, security men, attached to the same Administrative Reception, where the last screening always takes place, were said to have told him that he could not go beyond the point with his weapon.
In the process of submitting the weapon to operatives, the gun went off.
The incident occurred shortly after Jensen, who was accompanied by the Ambassador of Denmark to Nigeria, Mr. Torben Gettermann, and other Danish embassy officials, scaled through the last security checkpoint.