Moustapha Ould Limam Chavi is charged with financing terrorism, sharing intelligence with terror groups, and giving them financial and logistical support, the official said on condition of anonymity.
"These groups carry out attacks against countries in the region such as Mauritania and attack others in terrorist activities," the source added.
Three other Mauritanian nationals believed to be influential members of al-Qaeda in the Islamic Maghreb (Aqim) are also wanted.
Ould Limam Chavi lived in Burkina Faso where he was involved in negotiations with Aqim for the release of Western hostages in the Sahel and Sahara. He is a former advisor to Burkina Faso's President Blaise Compaore.
Security officials close to the political leadership in Ouagadougou say he left Burkina Faso in 2011, while other source said he moved to Ivory Coast.
He is opposed to Mauritania's president and has recently called for Abdel Aziz' ouster after accusing him of "failing in his bid to root out terrorism".
Among the three other suspects is Hamada Ould Mohamed Kheirou who is believed to head an Aqim splinter group, the Movement for Oneness and Jihad in West Africa which claimed responsibility for the kidnapping of three Westerners - a man and a woman from Spain and an Italian woman - in a Sahraoui refugee camp in Algeria.
The other two, Elhacen Ould Khlil and Vawaz Ould Ahmed, are believed to be influential members of an AQIM branch headed by Algerian Mokhtar Belmokhtar, alias "Laouar" (the one-eyed).
Along with Mali, Algeria and Niger, Mauritania is confronted with rising insecurity due to attacks by Aqim and other criminal groups as well as widely available weapons from the conflict in Libya.
Aqim is involved in terror attacks, kidnappings of Westerners and various types of trafficking including drugs.
Overall 12 Europeans are being held hostage in the Sahel region, south of the Sahara desert.