An Australian surgeon and his wife who have worked in Burkina Faso for decades have been kidnapped by Islamic extremists in west Africa, the President of Burkina Faso has confirmed.

The couple, Ken and Jocelyn Elliott, were kidnapped in Baraboule near Burkina Faso's border with Mali on Saturday, President Roch Marc Christian Kabore told AFP. The couple's family said in a statement last night that their whereabouts were unknown.

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