It is currently the responsibility of the minister of post-secondary education, training and labour.
The government says the proposed changes to the Human Rights Act are in response to recommendations made in recent years.
It says the commission had recommended the government look into the issue in 2008.
Last year, an independent review of legislative officers recommended making the commission the sole and final authority on initiating boards of inquiry.
Martine Coulombe, minister of post-secondary education, training and labour, says the changes would give more independence to the commission.