"The serious thing is that it could be part of organized crime to use stolen visas," Migration Board investigator Gunnar Fröberg told SVT, adding that each visa stamp could fetch around $20,000 on the black market.
So far, the investigation has not been able to link anyone to the suspected theft.
This is the second investigation in which the Embassy has been involved in such a short period of time. Earlier this year, a former staff member was investigated for accusations of having wrongfully issued around 70 visa documents to Afghan citizens during his time at the embassy, in 2015. The man, who was discharged from his position, denies the allegations.
"We don't trust him any longer," Migration Board regional director Magnus Rodin said then, admitting that the situation, where officials intentionally violate the rules and grant permits on false grounds was "extremely serious."
Later, people using the false documents reportedly sought asylum in Sweden, which invoked suspicions of professional human smuggling, a report by the Migration Board said.
A previous investigation by Swedish Radio revealed that the Foreign Ministry had information about problems with visa management at the embassy for a long time without taking any measures.
The embassy staff consists of personnel from the Foreign Ministry and the Migration Board, as well as local employees.
Earlier this week, a 34-year-old resident of the city of Örebro, previously suspected of terrorism, fraud and terrorist financing, testified about plans regarding attacks against Swedish cities, including Örebro and Stockholm. He also provided the authorities with information about Daesh (ISIS/ISIL) recruiters in Sweden, Swedish Radio reported.