Amisom identified some of the six as Aden Bale (commander of Leego), Sheikh Mohammed who was second in command in Janaale and Mohammed Abribao (al Shabaab judge in Janaale).
The others were named as Hassan Ali, chief Amnyat of lower shabelle region, and yemeni IED expert Abu Islam.
Sector One commander, Brigadier General Sam Okiding said the deaths bring to seven the number of commanders killed by the allied forces in one week.
"The Mission and the the Somali National Army have intensified the war against al Shabaab. The are more frequently resorting to hit and run tactics to avoid direct contact with Amisom and remain relevant," said Okiding.
He said operations to open the main supply route to Janale, and clear improvised explosive devices, have extended into the town.
"The clearance activities are meant to ease the movement of the population and goods," he said.
The forces killed al Shabaab commander Abdirashir Bugdube in Janale on April 2.
Sector One troops who were on patrol intercepted al Shabaab's technical vehicle on Mogadishu-Barawe Road. It was ferrying IEDs, grenades and bomb detonators.
A senior leader of the al Qaeda-linked militant group was killed in a US air strike targeting him on March 31, Pentagon spokesman Peter Cook said on Monday.
Hassan Ali was a member of al Shabaab's security and intelligence wing, and was involved in the planning of high-profile attacks, Cook said.