He faced the possibility of arrest because of an International Criminal Court warrant on charges of genocide.
A South African court ordered Mr Bashir to stay in the country while it decided if the warrant should be carried out.
But before the court ruled, Mr Bashir flew out of South Africa and returned home.
Sudan's president was in South Africa for an African Union summit and the government was aware that it may have been obliged to arrest him as a member of the ICC.
South Africa's Sunday Times newspaper quotes a government source as saying that at a meeting of security ministers it was agreed that South Africa would protect him "even if it meant flouting court rulings and undermining the constitution".
In a statement, the government "categorically denies there was a secret meeting" and adds that it will give the court an explanation of how Mr Bashir came to leave the country.
The High Court has given the government until Thursday to reveal how he was allowed to depart.
Source BBC
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