The fund, financed by the state of Senegal and the country's backers, comprises 1,000 billion CFA francs ($1.64 billion / 1.5 billion euros).
More than three quarters of the fund has so far been spent.
Judicial investigators have been ordered to make "preliminary investigations," prosecutor Amady Diouf said in a statement.
The affair follows a report in December by the national audit office into the so-called Covid-19 Impact Fund.
Opposition politicians and civil society groups have raised an outcry over the fund's management, although authorities say questions about spending irregularities concern less than one percent of its holdings.