The federal government says it is treating the suspected kidnapping of an Australian couple kidnapped in the West African nation of Burkina Faso "very seriously".

Surgeon Dr Ken Elliot and his wife Jocelyn were kidnapped in Baraboule, near the Burkina Faso's borders with Niger and Mali, on Friday night.

A spokesperson for the family said Dr and Mrs Elliot have worked in the Burkina Faso town of Djibo since 1972, where they run a 120-bed surgical clinic.

Dr Ken Elliot. (Supplied)

Dr Elliott is the only surgeon at the facility.

"They have dedicated their lives to providing medical relief to people in the remote northern area of Burkina Faso," a statement on behalf of the family read.

"Their commitment to the local people is reflected in the fact that they have continued there with only a few holidays since 1972. They are held in high esteem by the local people.

"Recent news from the country indicates an alleged abduction of Ken and Jocelyn on Friday night, however no reason is yet given for this and their whereabouts is still unknown."

Dr Elliot and his wife have worked in the African nation since 1972. (Supplied)

Dr Ken Elliot treats a child in Burkina Faso. (Image: GBS Institute)

A statement from the office of Warren Truss, Acting Prime Minister while Malcolm Turnbull is overseas, said the government was working with local authorities to find the couple.

"The Australian Government is taking the suspected kidnapping of two Australians in Burkina Faso very seriously," the statement read.

"Our thoughts are with the family of the Australians at this difficult time and we ask all to respect their request for privacy.

"However, I can say that we are working with local authorities through our High Commission in Accra, Ghana, which is responsible for Australian interests in Burkina Faso."

Malian Islamist group Ansar Dine said the couple were being held by members of the group "Emirate of the Sahara", who are linked to Al-Qaeda.

A spokesman for Ansar Dine, Hamadou Ag Khallini, told AFP in a brief phone message that the couple were alive and more details would be released soon.

An interior minister confirmed to AFP the couple kidnapped in the country's north were Australian, not Austrian as previously thought.

A Burkinabe intelligence source told AFP the Australian couple were in their 80s from Perth who had lived since 1972 in Djibo, near Baraboule.

The kidnapping comes as at least 26 people, mainly foreigners, were killed during an attack on a luxury hotel and restaurant in the capital Ouagadougou.

A total of 126 people were freed, 33 of them wounded, from the four-star Splendid hotel after security forces retook the facility and nearby Cappuccino restaurant on Saturday over 12 hours after the attack began, Interior Minister Simon Compaore told AFP.

The assault on the two venues, popular with Westerners and UN personnel, was crushed by midday but the police and military were still combing the area for other suspects, a security source said.

Communications Minister Remi Dandjinou gave a provisional figure of 26 killed and announced three days of mourning. The French foreign ministry gave a figure of 27 dead "and around 150 injured".

French special forces take up positions outside the Splendid Hotel in Ouagadougou. (AAP) (AAP)

Compaore said "three jihadists – an Arab and two black Africans – have been killed". The security source said four jihadists were killed, two of them women, and the victims were of 18 nationalities.

Al-Qaeda in the Islamic Maghreb (AQIM) claimed the attack on behalf of an affiliate, saying the strike on the former French colony was in "revenge against France and the disbelieving West", according to a statement carried by US-based monitoring group SITE.

AQIM said the gunmen were from the Al-Murabitoun group of notorious Algerian extremist Mokhtar Belmokhtar.

The attack will heighten concerns that jihadist groups are casting their net wider in search of targets in west Africa, two months after a siege at a luxury hotel in neighbouring Mali, where 20 people were killed, against mostly foreigners.

AQIM and Al-Murabitoun jointly claimed that attack.

President Roch Marc Christian Kabore, who took office just last month, a year after a popular uprising ousted longtime leader Blaise Compaore, called on his fellow citizens to show "courage".

Burkina Faso has "never caved in under any circumstances and it's not going to start now," he said.