Target at Cooleman Court will close by mid-2021 but it appears the stores in Canberra Centre, Belconnen and Tuggeranong will be spared.
Across the region, Goulburn's Target will remain, while the Target stores at Yass and Tumut will be converted to Kmart. The Cooma store will close.
More than 150 Target stores will either close altogether or be converted to Kmart stores in a major restructuring by owners Wesfarmers, the company announced on Friday.
The company said 125 Target stores will remain compared with the 284 currently in existence.
Weston Creek Community Council chairman Tom Anderson was informed of the decision to close the store in Cooleman Court on Friday evening.
He said the council was shattered and surprised.
"This is more than disappointing for our community, it is a blow to the body," Mr Anderson said.
"It is also a blow for those who will lose their employment at this time, and for the centre itself with the largest retail shop closing.
"Surely this is not the time for a conglomerate like Wesfarmers to make these decisions. Just another blow to the local community following the closure of the Commonwealth Bank branch in March."
In a letter to the Weston Creek Community Council, Target Australia managing director Marina Joanou called the decision regrettable.
"We are commencing an extensive process of reaching out to our stores and those team members most impacted by the changes to explain what it means for them," she said.
"We recognise that these actions will have a significant impact on a number of our team members and are committed to supporting them through this process."
Staff would be given "priority consideration" for new roles created in the business, she said.
"In addition, Wesfarmers has established a cross-divisional working group to identify redeployment opportunities for affected team members, including in Bunnings and Officeworks."