Crossroads Christian Communications, a group that produces television programs, received $544,813 in federal money to help dig wells, build latrines and promote hygiene awareness in Uganda through 2014.
Crossroads recently listed homosexuality as a perversion and a sin on its website, although the post disappeared after questions were asked about it.
Canada's International Co-operation Minister Julian Fantino said he is reviewing the organization before further payments are made.
In 2009, an anti-gay bill in Uganda's parliament proposed death for some homosexual acts. A new version of the legislation doesn't include the death penalty, but proposes banning gay marriage, counseling gays and punishing those who promote gay culture.