The briefcase, which police believe was stolen, was reported missing last Monday by the Spain's General Department of Foreign Affairs.
The missing visas are numbered and bear codes ranging from ESP008857001 to ESP008857500, according to Spanish daily La Vanguardia.
This will make it more difficult, but not impossible, for them to be used illegally.
Police attached to the Spanish embassy in Nigeria are working with local authorities to track down the visas.
The diplomatic case was stolen from the airport before it could be collected by accredited staff. Its eventual destination was supposed to be the Spanish consulate in Lagos.
The visas are said to be extremely valuable on the black market in Nigeria as they are the key to entering Europe and travelling between countries that are members of the Schengen Area.
Anti-terrorist police in Europe are currently on high alert and monitoring flights in and out of the area after the recent terrorist attacks in Paris.
The theft of the visas has occurred a time when the actions of the armed jihadist group Boko Harem have intensified in Nigeria.