Though theoretically only the number two in the defence ministry, Inda'adde was seen as the man in charge and a key member of the embattled Western-backed transitional federal government's security apparatus.
"After seeing the government fail to deliver on the commitments it made when it was established, I decided to quit and I am no longer part of the government," Inda'adde told reporters in Mogadishu.
Inda'adde, a powerful clan and militia leader, said the government had failed to stabilise the country.
Since being elected in January 2009, moderate Islamist President Sharif Sheikh Ahmed and his government have failed to pin back an insurgency which controls two thirds of the country.
Inda'adde submitted his resignation along with two other government members, said officials in the prime minister's office on condition of anonymity.
"The state minister for defence and two other ministers who are not currently in the country submitted their resignation letters to the prime minister today," one official said.
The two other government members he said had tendered their resignations are higher Education Minister Mohamed Abdullahi Omar and State Minister for the Presidency Hassan Maalim.