The Finance Division issued an office memorandum yesterday to abolish the "Secret Service Expenditure" of the ministries and foreign missions.
The decision will not affect the secret funds of intelligence agencies, The News daily reported.
Sixteen ministries, including the Interior and Information Ministries, had "massive secret service funds" that they used for purposes not publicly known. These funds were not open to routine audit, the report said.
The decision to abolish the Secret Service Expenditure was taken by the newly elected government of Prime Minister Nawaz Sharif to curb corruption and for good governance.
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It is an "open secret" that the Secret Service Expenditure was "used by the government to win loyalties of their opponents, project its image, target its foes or on such matters which do not fall in the category of good governance", the report said.
The Finance Division's notification said: "The budget provision under head Secret Service Expenditure available with ministries/division/departments/organisation, except intelligence agencies, for current financial year shall be surrendered immediately."
Experts said the decision was aiming at curbing corruption and corrupt practices by blocking all back channels for using public funds.
In his budget speech in the National Assembly yesterday, Finance Minister Ishaq Dar said the country had come to know in recent days that in the name of secret service expenditure, a long list of ministries and departments had been incurring expenditures that were excluded from audit.
"This exclusion from audit was meant for such expenditures incurred by agencies connected with the national security," he noted.