Although the monies have hit their accounts already, and some of them have reportedly used them in purchasing things, a High Court has ordered the lawmakers to repay a sum of $5,000 each they received.
The court gave the order after independent MP Gerald Karuhanga filed a case over the issue.
Karuhanga and a few MPs rejected the money when the parliament approved the package totaling around $2.6m, reports say.
The payment was condemned by many including a prominent lawmaker and presidential hopeful Bobi Wine who described it as a shameful scheme.
The country’s President Yoweri Museveni was vehement in condemning the controversial payment on Wednesday, referring to it as “morally reprehensible”.
“It is morally reprehensible for MPs to give themselves money for personal use when the country is in such a crisis; totally unacceptable to me and the NRM.
They have entered themselves into a trap and the best way out is to donate the money to the districts where they come from,” he said on Twitter.
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“I heard that some MPs went and bought things, you are not a purchasing officer of the state. This is public money, not personal money, if you spent it wrongly you will pay it back with your salary; this will be sorted out by the Auditor-General,” Museveni warned.
The High Court had already issued an injunction over the scheme but the speaker of Uganda’s parliament said the money had already been paid into MPs’ bank accounts.