Section 5D. The comptroller shall determine, based on procedures established by the secretary of administration and finance, the amount expended during the fiscal year from each fund, other than the General Fund, for indirect costs and for the compensation of state personnel. On the basis of said determination, the comptroller shall charge each fund an amount for indirect costs and for fringe benefit costs attributable to compensation paid from the other funds, based on an indirect costs rate and on a fringe benefit rate to be set annually by said secretary. The amount so charged shall be credited to the General Fund. Upon approval of the secretary, and subject to regulations established by the secretary, the amount of indirect costs, either in whole or in part, charged to an account may be waived. The costs of fringe benefits shall be recovered in cash.

The comptroller shall make charges to recover the commonwealth indirect costs and the cost of fringe benefits provided to or on behalf of any person paid compensation by a state agency, authority or public institution of higher education, or by any entity otherwise directly or indirectly receiving state funds, from any source other than a direct expenditure of an appropriation charged to a state fund subject to the preceding paragraph. The comptroller may establish such systems of periodic charges or billings as the comptroller considers necessary and appropriate to ensure the recovery of these costs. Any bill rendered for the purpose of recovery of these costs shall be payable to the comptroller within 30 days after receipt of the bill and all amounts so paid shall be credited to the General Fund.