Sudan's information minister has said that Sudanese President Omar al-Bashir flew out of South Africa on Monday, defying a high court order which banned him from leaving the country until an application calling for his arrest had been heard.

"Yes, he has left," Information Minister Ahmed Bilal Osman confirmed to Al Jazeera, saying that South Africa had always agreed not to arrest the president while he was in the country for the African Union summit.

"President Bashir is not a prisoner inside Sudan," he added, saying that the president was due to land back in Khartoum at about 6:30pm local time (15:30 GMT).

An interim order was made by the high court in Pretoria on Sunday, barring President Bashir from leaving South Africa, pending an application from civil society organisations calling for his arrest on an International Criminal Court warrant.

Earlier on Monday, Osman said the president would return to Sudan regardless of whether the high court ordered his arrest.

"The [South African] judiciary...does not have policemen... No one is going to arrest him."

The South African state broadcaster, SABC, reported at about 10:15 GMT on Monday that the president's plane had flown out of the Waterkloof air force base, on the outskirts of Pretoria.

News Just In: A diplomatic source has confirmed that Sudanese President Omar al Bashir has just left the country for Khartoum. #SABCnews — SAfm news (@SAfmnews) June 15, 2015

A lawyer appearing on behalf of the South African government, however, later told the high court in Pretoria that President Bashir was not on the list of passengers in the plane that left Waterkloof base.

Read more: Background on African Union opposition to the ICC

Prior to the president leaving the country, the high court in Pretoria was expected to decide whether to send Bashir to the International Criminal Court.

Al Jazeera's Fahmida Miller, reporting from Johannesburg, said that the Sudanese president's plane had been moved to a South African military base late on Sunday night.

She said that the defence force was not a party to the court case, meaning President Bashir would be able to fly from the base unobstructed.

If the plane has left as reported, the home affairs department could be held in contempt of court for failing to implement the conditions of the court order barring the president's exit, our correspondent reported.

Bashir, who is accused of war crimes in repressing an armed uprising in the Sudanese region of Darfur, was appeared in Johannesburg on Sunday for the AU summit.

The Hague-based ICC issued an arrest warrant in 2009, but Bashir denies the charges.

UN Secretary-General Ban Ki-moon told reporters in Geneva on Monday that the authority of the ICC must be respected and its decision implemented.

Before Sunday's court ruling was announced , the judge said the court would decide whether a South African government cabinet decision to host Bashir would trump the ICC arrest warrant.