The women were kidnapped in separate incidents on Thursday and Friday as they foraged for food in the latest attack on civilians by suspected Al-Qaeda extremists.
Suspected jihadists have kidnapped at least 50 women in Burkina Faso.
The government announced on Monday that 28 bodies had been found on New Year’s Eve in northwestern Burkina Faso.
Mr Guterres pointed out in his statement the doctrine of persona non grata does not apply to United Nations officials.
Burkina Faso’s military Junta government has prohibited French media outlet Radio France International (RFI) from broadcasting in the country.
The French embassy said Burkina Faso’s military police did nothing on November 18 as hundreds of protesters violently attacked the embassy.
UN deputy secretary-general Amina Mohammed says the growth of terrorism is a major threat to international peace and security, felt most in Africa.
The newly appointed Prime Minister Apollinaire Kyélem de Tambéla presented his cabinet in the capital Ouagadougou on Wednesday.
“We are not afraid to be shut. It would make us do much better. It would make our schools and hospitals do better.”
The latest restrictions took effect on October 18.
