Harper first promised the new branch of Foreign Affairs nearly two years ago during the last federal election campaign.
The announcement will be made at the Ahmadiyya Muslim community centre and mosque in Vaughan, Ont., a community north of Toronto.
The government's plan has been delayed for several months after it was revealed that Foreign Affairs Minister John Baird had trouble filling the top job.
Senior government sources told CBC News in the fall that at least two people had turned down the position of ambassador after being approached by Baird.
The foreign affairs minister, who is on a six-country tour of Latin America this week, will not attend the announcement.
Harper will be joined by International Co-operation Minister Julian Fantino, who represents Vaughan in the House of Commons, and Immigration Minister Jason Kenney, a key player in the Harper government's relationship with ethnic communities.
The new office is reported to have a price tag of $5 million, including $500,000 for operations.
NDP foreign affairs critic Paul Dewar said there are many questions to be answered on what role the office will play.
"It really is a question of at what cost to other areas?" said Dewar. "Are they going to come forward with other initiatives on human rights protections, democratic development?"
The idea of an office has not been without controversy over a possible bias and which religious communities it will represent.
In 2011, a closed-door meeting about the office, organized by the government, was criticized by some scholars after it turned out four of the six panellists being consulted were drawn from Christian religions, with the other two being Jewish and Ba'hai.
Around the same time, Baird went to Washington to meet with Suzan Johnson Cook, head of the U.S. Office of International Religious Freedom, which the Canadian office may be modelled after.
The U.S. office was put in place by the Clinton administration.