There have been issues of cronyism, nepotism, and corruption in the Ministry of Education, subject to performance audits focused on adherence to the Government’s procurement guidelines and contracts management. According to the opposition leader, the allegations are related to the misuse of public funds and to the “politically connected” persons who have been employed by the education ministry as advisers, “but are not doing any work”.

In order to fight corruption and discourage private schools to operate a cartel, the Supreme Court in Pakistan has not allowed an increase in school fees of more than 5% per year. Many directors of private schools took money from parents for security deposits and admission fees and earned profits on that money. An Auditor General report highlighted how in public schools some teachers received very good salaries, but they were not doing justice to what they receive while teachers in private schools earned far less amount but they perform better.

A former finance clerk is accused of embezzling $859,000 in funds that belonged to Esperanza High School’s student council. State auditors allegedly identified 270 checks made payable to the former finance clerk who oversaw the books while others were for two of the clerk’s relatives. According to the State auditors' bank records from 2005 to 2011, the total amount of embezzled funds is more than $1.5 million.

Sindh Anti-Corruption Establishment has found corruption and misuse of authority in Sindh Education Department district Jacobabad involving illegal inducting of hundreds of fake teachers, getting illegal financial benefits in the name of fake employees’ retirement, pension and death claims from department and life insurance company. The investigation continues after the fraud of millions of rupees has been reported, as well as the illegal role and abuse of authority from officers of the Education and Finance Departments.