The International Committee of the Red Cross said several aid agencies have been expelled from the country, while those that remain behind are hampered by security constraints.
Pascal Mauchle, the head of the ICRC delegation for Somalia, said all parties to the conflict must take "feasible precautions" to separate civilians from combatants.
"We are concerned about the devastating effects of the ongoing fighting on the civilian population," he said in a statement. "Attacks may be directed only against persons taking direct part in hostilities and against military objectives."
The humanitarian agency said it received roughly 5,000 war casualties at ICRC-supported hospitals in Mogadishu. That figure is 25 percent higher than recorded in 2009 in general and 72 percent higher for women and children.
Al-Shabaab, the al-Qaida backed militant group trying to create an Islamic state in Somalia, has declared war on African Union peacekeepers in the country.
"Every civilian who can is trying to flee bullet-scarred Mogadishu in search of safety," the ICRC said.