The plane operated by Badr Airlines landed safely in the Sudanese city of Port Sudan, the ministry said in a statement.
"The plane carrying 125 people from Khartoum to Jeddah had to make an emergency landing after its left engine caught fire," ministry spokesman Abdelhafiz Abdelrahim told AFP.
"The plane landed safely and there were no casualties."
He did not clarify what caused the fire.
Officials from Badr Airlines were not immediately available for comment.
The airline's cargo planes have regularly transported humanitarian aid for the World Food Programme, UNICEF and other international aid agencies, the company says on its website.
Apart from operating flights across Sudan, Badr Airlines operates regular flights to Cairo, Jeddah and Juba, the capital of neighbouring South Sudan.
Accidents are common among Sudan's ageing fleet of aircraft, and many countries ban several Sudanese airlines for safety reasons.
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