"The state of emergency has nothing to do with the demonstrations as those who are demonstrating are Sudanese citizens," the official said on Wednesday.
Over the past months, the rapidly deteriorating economic situation in Sudan has prompted citizens to take part in mass protests.
Ibn Auf, who also serves as the defense minister, has already shown a conciliatory tone to the youths taking part in the demonstrations.
"The emergency is meant to curb smuggling that is destroying our economy."
Sudanese officials have regularly said that widespread smuggling of gold and other commodities across the country have severely damaged the economy.
On Tuesday, four Western countries, namely the United States, Britain, Norway and Canada, expressed concern about the state of emergency.
In a joint statement issued by their Khartoum embassies, the countries called on court officials in Sudan to release those detained during anti-government demonstrations.
"The return to military rule does not create a conducive environment for a renewed political dialogue or credible elections" in Sudan, the joint statement said.