Ministers have offered reassurances that money given to the national Malawi appeal in Scotland will go directly to aid projects.
The executive said money would go to projects in the community
The country has not been included in the 18 African countries qualifying for immediate debt relief under a G8 ministers' plan.
However, it will qualify for debt relief in 12 to 18 months.
The Scottish Conservatives have expressed concern about the handling of aid money sent to Malawi.
The Scottish Executive said First Minister Jack McConnell made a point of discussing institutional corruption with President Dr Bingu wa Mutharika during his tour of Malawi last month.
Mr McConnell said he was reassured that the president, who has been in office for 18 months, was making strenuous efforts to root out corruption.
Conservative MSP Brian Monteith said the decision to delay the Malawian debt relief raised concerns about the public appeal launched by Mr McConnell last month.
Debts wiped out
However, an executive spokesman said that all of the money would go directly to aid projects like hospitals, schools and orphanages.
It would not be channelled through government departments, the spokesman said.
Bobby Anderson, chairman of the Scottish Malawi Appeal, said: "I think people can be reassured that the distribution of the funds raised through the appeal are going straight to the community organisations in Malawi, through NGOs, charities and churches.
"None of it, not a penny of it, is going to the Malawi Government."
At the weekend, finance ministers from the world's eight richest countries reached a deal to wipe out 100% of the money owed to them by 18 countries immediately, estimated to be $40bn.
Malawi is one of nine countries, owing an estimated $11bn, who will see their debts wiped out in 12 to 18 months.