Wagadou, near Mauritania's border, is an area where al-Qaeda in the Islamic Maghreb (AQIM) are known to operate.
Earlier this month, Mali and Mauritania agreed to lead a joint operation to tackle the al-Qaeda offshoot.
'Wounded evacuated' The attack took place at about 1745 local time (1745 GMT) on Friday and involved air strikes, according to a Mauritanian source cited by AFP news agency.
The source said the "terrorists" had struck back with "heavy weapons".
Al-Qaeda in the Islamic Maghreb
- Emerged during Algerian war in the 1990s as Salafist Group for Preaching and Combat (GSPC)
- Declared allegiance to al-Qaeda in 2006, changing its name accordingly
- Operates in the lawless Sahara desert regions between Niger, Mauritania, Mali and Algeria
- Carries out frequent terror attacks and kidnappings for ransom or to demand the release of prisoners
- Killed some 26 people in an attack on UN offices in Algiers in December 2007
- Suspected members have been arrested in several Western European countries
The Malian source said helicopters from Mali had been used to evacuate the wounded from the area.
Regional governments has been on high alert since the death of al-Qaeda leader Osama Bin Laden in Pakistan in May, amid concern that affiliated groups might plot a revenge attack.
Al-Qaeda in the Islamic Maghreb (AQIM) has staged attacks and kidnapped Europeans in the region.
It emerged from Islamist groups fighting in Algeria in the 1990s.