"Senator Meredith is no longer a member of the caucus," Stephen Lecce, a spokesman for Harper, said late Wednesday night.
The development comes as the Toronto Star reported Wednesday night that an 18-year-old woman alleged she had an inappropriate sexual relationship with Meredith, which began when she was 16.
The teen told the Star the relationship begin with chats online that became suggestive in nature, and progressed to include sexual intimacy, including intercourse after she turned 18.
The Criminal Code defines the age of consent in Canada as 18 if sexual activity occurs in a relationship of authority, trust or dependency.
Meredith, 50, is an ordained minister at a Pentecostal church in Vaughan, Ont. He ran unsuccessfully for the Tories in Toronto Centre in a 2008 byelection.
The Senate confirmed last week it had undertaken a workplace review in February amid rumours of harassment and bullying in Meredith's office. No formal complaint was made.
The concerns related to at least four employees.