Prime Minister Stephen Harper boycotted the Commonwealth summit last year in Colombo, Sri Lanka, because of concerns about the government's human rights record.
Canada would normally contribute $10 million per year to the secretariat over the next two years, but Baird says that money will be directed elsewhere.
He says Canada's voluntary contribution will instead go towards other programs that promote Commonwealth values.
The Harper government has won praise from international human rights watchdogs for pushing for an independent investigation of the events surrounding the end of Sri Lanka's 27-year civil war in 2009.
Government forces and Tamil Tiger rebels have been accused of committing atrocities, but repeated calls for an independent investigation have fallen on deaf ears in Colombo.
"Canada remains deeply concerned about the absence of accountability for alleged serious violations of human rights and international humanitarian standards in Sri Lanka," Baird said in a statement.
"We will reallocate the funds to assist in combating the practice of child, early and forced marriage, and help Commonwealth civil society advance the promotion of human rights."