Under an ICO ruling, Joyce Refearn. the council's chief executive, has given a formal undertaking that she will take steps to improve the council's IT security.
The data loss happened when a laptop - which contained personal data on children and young people in Wigan's schools and which was normally stored in a locked office - was stolen in January of this year. The council only revealed details of the loss in March.
As part of the undertaking with the ICO, Wigan council is now ensuring all of its portable computers and mobile devices used to store and transmit data are fully encrypted.
According to the council, its staff are also being trained in the appropriate storage and use of personal data.
Commenting on the ruling, the ICO's head of enforcement, Sally-Anne Poole, said: "I strongly advise organisations to avoid instances where employees can download large volumes of personal information."
"This incident could have been averted if the data was simply accessed from the main council computer network. Storing information on portable devices is unnecessarily risky."
"I am pleased the council has taken action to guard against security breaches of this nature."