It says the forms had their initial data entered into the system but may have been packed away with processed forms and are yet to be found.
It says it has contacted affected applicants and it will notify the Office of the Privacy Commissioner.
Meanwhile, the government says it has handed out more than HK$10 billion dollars under the scheme for almost three million approved applications. The cash handout scheme was introduced in March last year following intense criticism on the budget.
Hong Kong residents aged 18 or above are entitled to the money if they don’t own property or benefit from government allowances.
The scheme has also come under fire for its complex application procedure and administrative costs.