The 2006 Comptroller and Auditor General (CAG) report has indicted the state education department for irregularity in releasing Rs 27. 35 lakhs in Shillong and Rs 90.36 lakhs in Nongpoh to teachers of unauthorised schools under the SSA. The CAG report says that during November 2003 to March 2004, the Joint District Mission Coordinator based in Shillong paid Rs 20.18 lakhs from the SSA fund for salary of 104 lower primary school teachers and Rs 7.17 lakhs to 25 unapproved lower primary schools.

In November 2005, the state Government admitted of the illegality in releasing Rs 27.35 lakhs and assured that efforts were on to recover the money. According to the Special Officer of the department, Rs 10.97 lakhs had been recovered till August 2006.

Between 2004-2006, CAG revealed that the State Project Director had released Rs 90.36 lakhs to the Nongpoh District Mission Coordinator (DMC) for payment of salaries to teachers in 132 unapproved schools (60 primary and 72 upper primary schools). Similarly, during 2003-2005 the State Mission Authority sanctioned Rs 52.26 lakhs to the DMC in Shillong for payment of salaries to teachers engaged in 88 unapproved new schools.

The CAG said that non-approval of the schools was indicative of the fact that these were not under the SSA.