Gift of the Givers says it and its personnel did not apply for Syrian visas upon entering the country, as they received permission from the civilian-controlled region they were working in.
Media reports indicated that missing South African Shiraaz Mohamed and the Gift of the Givers humanitarian mission may have entered Syria unlawfully.
The Syrian Embassy's Charge d'Affaires told Eyewitness News on Friday that Mohamed had not received visas from the Syrian embassy and presumably entered into the civilion-controlled region through the Turkish border.
Gift of the Givers spokesperson Imtiaz Sooliman told News24 that Syria is at war, and therefore the country is divided into the "Syrian Government section and non-Syrian Government section".
"The non-Syrian Government section controls the north. We obtain (sic) permission from the Turkish government to cross their border into Syria and the permission of the non-Syrian Government civilians to operate in their area," Sooliman said.
"It was these civilians who gave us a building to convert into a hospital and gave us additional land to expand our hospital."
Sooliman said all aid agencies and media can enter the North without any visas because that part of the country did not belong to the Syrian Government any longer.
He also emphasised the South African government passed two motions of commendation in Parliament in recognition of their work inside Syria.
'SA citizens must comply with the law'
Department of International Relations spokesperson Clayson Monyela told News24 on Saturday that the law should be followed when applying for a visa to another country.
"Our stance has always been if a country requires you to get a visa before you enter that country, South Africans need to comply with that," Monyela said.
"That's what the law says. We wouldn't encourage anyone to break the law despite what the purpose of their mission is."
Monyela said that although Syria's circumstances are unique, the government still holds the legal authority within its borders.
"There is a government in Syria. I don't know if international law and common sense allows us to compartmentalise a country that still has a democratically elected government, despite what the circumstances are.
"If there is a requirement in terms of the law to get a visa, we will encourage South Africans to comply with that."
The Syrian Embassy could not be reached for comment on Saturday. -- News24Suggest a correction