"The church is hugely unrepresentative in relation to gender... women constitute the majority in our pews but the reverse is true at every level of leadership, lay and ordained," Makgoba said in a statement.
"The roles of men and women alike, of every culture, were distorted by apartheid. We need to develop appropriate spiritualities for us all, for contemporary living... that are also channels of healing for the legacies of our brutalising history."
Makgoba was delivering a speech at the three-yearly provincial synod of the Anglican church in Benoni.
He also expressed his views on conscription - describing it as having a "dehumanising effect... on a generation of young men barely more than boys".
"Many are still wounded from that time... from their time in Namibia and Angola and need to be able to speak and find healing. Our society makes this almost impossible."
On the issue of the position of homosexuals in the church, Makgoba said: "For us what has mattered most is being centred on Christ, agreeing on the central matters of who Jesus is and the salvation he brings and therefore recognising one another as being united in him, and, in consequence, with each other."
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