"The sanction operation, which is especially directed against (Sudan’s) national institutions, will not help achieve peace," the ministry said in a statement.
The ministry further said that justifying targeting the three economic institutions for their affiliation with the Sudanese Armed Forces (SAF) is "surprising and deplorable."
"The right and duty to defend the country necessitate the SAF to seek to achieve sufficiency in defensive equipment, and all laws guarantee the right to self-defense," the ministry added.
On Monday, the European Council adopted sanctions against six entities affiliated with the SAF and the paramilitary Rapid Support Forces (RSF), including asset freezes and prohibition of the provision of funds or economic resources, directly or indirectly.
It said in a statement that the six entities were responsible for "supporting activities that undermine the stability and political transition of Sudan."
Sudan has been witnessing deadly clashes between the SAF and the RSF since April 15, 2023.
More than 12,000 people had been killed, and over 7.4 million had been displaced inside and outside Sudan since the fighting broke out, according to earlier estimates by the UN Office for the Coordination of Humanitarian Affairs.