The Tuaregs and Islamists groups that took control of the towns of Gao, Kidal and Timbuktu have been accused of raiding and looting houses and hospitals, with residents hiding in fear.
A military junta ousted the government following its failure to tackle a two-month Tuareg rebellion in the north of the country. Mali has been torn by tensions between Tuareg separatist groups and the government for decades.
Political instability has benefited the rebel groups as the National Movement for the Liberation of Azawad (MNLA), helped by the Islamist group Ansar Dine, have now taken control of the towns of Gao, Kidal and Timbuktu.
Residents in Goa have spoken out about the chaos that engulfed the city in the takeover.
They report the rebels raiding and looting houses, hospitals, NGO offices and government buildings.
"People are hiding at their homes unable to leave. No trucks are arriving with further supplies. What will we do when our stocks run out? The hospital is closed and doctors have fled. It is complete desolation and despair. We can only turn to the international community for help," Issa Mahamar Touré, president of the youth association in Gao, told Integrated Regional Information Networks.
Ansar Dine, which is now in control of Timbuktu, said it will impose Sharia law and ban alcohol, music and western clothing.
Residents are scared they will be forced to live under strict Islamic rules.
Although Mali is suffering from drought in the north of the country, the armed attacks have led to most NGOs' work being halted.
The offices of the World Food Programme, Catholic Relief Services, Oxfam, and the International Committee of the Red Cross have all been targeted. There are also fears that aid workers could be attacked.
The population remains in desperate need of food, water and medicine at a time when humanitarian aid is being further hampered and the number of displaced people is only set to increase. According to the United Nations, more than 200,000 people have already fled Mali since the beginning of the year.
United Nations High Commissioner for Refugees spokesperson Melissa Fleming said at least 400 refugees from Mali are crossing into Burkina Faso and Mauritania every day.
"They are fleeing because there is generalised violence, but also because mayhem is increasing in towns and cities. While in flight, they are being targeted by armed men who take their cars, their money and other personal belongings as they flee for Burkina Faso and Mauritania. They are also reporting a shortage of food," Fleming said.
"Mali itself is one of the top drought affected countries in the Sahel region, I think it is number two. They are reporting steep price rises and concern about sustaining themselves," she added.
Reports of rape have also started to emerge, mainly in Timbuktu and Gao.
As vandalism increases, organisations are warning violence could spread further.
The Economic Community of West African States (Ecowas) has imposed a set of sanctions against Mali and members of the military junta, with neighbouring states also closing their borders.
Ecowas has set a 9 April deadline for the junta to hand over power. Coup leader Amadou Sanogo Said said his group will hold a national convention on 5 April to determine the country's future.
Some banks have already run out of cash and the sanctions on Mali mean a lot of government workers will not be paid in April. Analysts have warned that the cash shortage, coupled with increasing food and fuel prices, may lead to further chaos.