MTN Uganda, a unit of the South African telecoms firm, said security personnel had raided its data and disconnected four of its servers.
The firm said in a July 3 letter to the State-run telecommunications regulator that it had "reported to police a case of illegal intrusion into the data centre and the disconnection of the four information servers."
The regulator Uganda Communications Commission (UCC)'s top official confirmed to Reuters receipt of the letter.
"Yes, yes I have seen on social media that letter. I don't know who leaked it but I received it, yes. They were complaining that they were raided," Godfrey Mutabazi told Reuters.
MTN Uganda is the country's largest telecommunications firm with a subscriber base of above nine-million.
In the letter the company said men who said they were from Uganda Internal Security Organisation (ISO), a security agency in charge of domestic intelligence, had on July 2 also kidnapped an employee of its contractor, Huawei Technologies.
The security personnel then forced the employee to grant them access to a data centre in a suburb of Kampala where they then proceeded to forcefully disconnect four servers.
"This incident poses a serious security risk to our telecommunications infrastructure and customer data," MTN said.
Police spokesperson Emirian Kayima told Reuters he was "aware of the letter but I am verifying at the moment. I can't comment for now."