French diplomats said they would set up office in the grounds of the larger British consulate in the city which is regarded as being in a more secure area.
Karachi has witnessed a number of attacks against foreign targets in recent months, including a bomb attack in May which killed 11 French nationals.
The attacks have been blamed by the Pakistani authorities on militant groups angry over President Musharraf's backing for the US-led campaign against the Taleban and al-Qaeda.
Security worries
A spokesman for the French consulate, Ata Ansari, said French soldiers guarding their own consulate would be sent home, and the French would rely on British-arranged security.
Security experts had decided that the existing consulate building on Ali Bogra road was unsafe because it was in a residential area, Mr Ata said.
He said it was not possible to close roads in the area indefinitely as required for security purposes.
The French consulate shut down its visa section shortly after the May bombing.
In that attack, a car packed with explosives was detonated near a bus carrying French naval engineers outside the Sheraton Hotel.
A total of 14 people died in that incident.
In June, 12 people were killed when a bomb went off outside the US consulate in Karachi.
Earlier this month, the Pakistani authorities said they had arrested three men in connection with the attacks.
They also said they had arrested a member of the security forces who had allegedly plotted to assassinate General Musharraf.
President Musharraf has pledged to clamp down on the activities of extremist groups, banning a number of them and arresting their members.