Tuaregs in Gao say Al-Qaeda planted landmines around the city, while Ansar Dine Islamists have attacked the Sidi Yahia mosque in Timbuktu.
The northern city of Gao, home to 90,000 on the banks of the River Niger, is now controlled by the Movement for Oneness and Jihad in West Africa (MUJAO), a group affiliated to the Al-Qaeda Organization in the Islamic Maghreb.
Mujao is also linked to the Ansar Dine movement, an Islamic group which controls the city of Timbuktu.
The Tuaregs members of the separatist movement National Movement for the Liberation of Azawad (MNLA) initially backed the Islamists' rise to power but clashes between the groups ended their alliance.
Now the MNLA claim Al-Qaeda and their splinter group MUJAO have planted land mines around the city to prevent residents from fleeing.
"A lot of people were trying to flee but the Islamists prevent them from leaving the town",
Mossa Ag Attaher, a spokesman for the MNLA told AFP.
AFP says the news was confirmed by a security source based in Bamako.
Sidi Yahia attacked in Timbuktu
In Timbuktu Ansar Dine rebels proved they are still determined to destroy the city's Muslims shrines.
Members of the Islamist group which is now in control of much of northern Mali have attacked the door of the Sidi Yahia mosque.
The 15-centrury site is one of Timbuktu's three great mosques.
The BBC spoke to residents of Timbuktu who confirmed the attack.
The door that was broken was sealed as it leads to the tomb of saints.
Some of the witnesses and local people cried when they saw the damage, AFP say.
Ansar Dine had warned they intended to destroy most of the city's ancient shrines as they consider them as idolatrous.
The spokesman said Sharia did not allow the building of tombs taller than 15cm (6 inches), the BBC report added.
The group had already destroyed the tombs of Sidi Mahmoud, Sidi Moctar and Alpha Moya on 30 June. The following day, they attacked Cheikh el-Kebir's mausoleum in front of residents, along with another two sites.
Fatou Bensouda, the chief prosecutor for the International Criminal Court urged the group top stop destroying the historical sites and warned them the criminal acts could constitute a "war crime".
The UN cultural agency Unesco, Mali's government and UN Secretary-General Ban Ki Moon also called on the rebels to stop that attacks but the group seems set to continue on its destructive path.
Unesco has said it fears some of the city's valuable artefacts and books could be smuggled out of the country and sold on the black-market.