They included 10 senior executives handed five-figure payouts while a regime which left thousands of students waiting for their loan and grant payments was being developed.
The Liberal Democrats, who uncovered the sums, described them as "outrageous" and said rewarding failure was unacceptable.
Figures released under the Freedom of Information act showed that staff at the SLC, which is based in Glasgow, were handed bonuses totalling £1,893,500 in 2008/09.
Three bosses received £21,000 bonuses, while two got payouts of £15,000 and five were given £10,000.
Some 1603 of the SLC's 1876 staff picked up rewards.
The figures also showed senior executives racked up an expenses bill of £110,596.31 - £28,000 more than the previous year. In total staff claimed more than £1.2m in expenses, up from £793,000 in 2007/08.
Ministers ordered an inquiry after almost 150,000 students who had applications approved were left without funding at the start of the new academic term.
This year was the first time freshers applied directly to the SLC for grants and loans and the new arrangement has been beset by problems as it struggled to cope with demand.
Lib Dem universities spokesman Stephen Williams said: "It is absolutely outrageous that the Student Loans Company, which has acted so incompetently this year, has been paying out these massive bonuses.
"While students have been left struggling to make ends meet, the company's top executives have been enjoying five-figure bonuses.
"Some of these pay-outs are more than many people earn in a year. Rewarding failure in this way is totally unacceptable."
The SLC said the company "operates a bonus scheme structure to reward hard working staff".
"Employees' objectives are monitored throughout the year and they are given an individual performance assessment at the end of the year," it added.
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