Cabinet spokesman Muhammad Mutawa said $23 million will go to a retirement fund for civil servants and the remainder to a social security fund for private sector employees.
Mutawa has also announced on Sunday that three ministers are due to be questioned before a house committee by the end of the month.
The investigation will focus on alleged irregularities and a possible ministerial role in waiving loans to finance a number of projects.
The government had already ordered a company building the Bahrain Exhibition Centre to immediately repay a loan it received from the funds.
Manama has also told the National Hotel Company to repay the interest on another loan from the funds.
MPs in January demanded the right to question Labour and Social Affairs Minister Majid Al-Alawi, who chairs the board of the social security fund.
Minister without portfolio Abd al-Nabi Al-Shuala and Finance Minister Abd Allah Saif, who runs the civil servants' fund, are both also to be called before the committee.
The questioning will mark the first time Bahrain's 40-member parliament has grilled ministers since it was restored in late 2002 as part of reforms which turned the Gulf state into a constitutional monarchy.