The rebuttal from the Scottish Catholic Education Service came after anti-sectarian charity Nil by Mouth included the suggestion in an action plan to tackle the issue.
As part of its proposals, Nil by Mouth called for the Scottish Government to engage with councils over the possibility of building more shared campuses across Scotland – where Catholic and non-denominational schools share facilities. The charity also suggested more twinning links between schools.
However, Michael McGrath, director of the Scottish Catholic Education Service, said the problem of sectarianism was rooted in communities, not schools.
He said: "Catholic schools already promote tolerance, respect and diversity very effectively. Nil by Mouth's proposals strike me as more examples of failed projects and tokenistic gestures.
"Every school already has good contacts and arrangements with other schools in their area. Artificial twinning of schools is not helpful or constructive. It's a sop to officials so they think something is going on.
"We need to focus more on the good work arising naturally from within schools."
Peter Kearney, director of the Catholic Media Office, said Nil by Mouth's plans showed how the debate of the sectarian issues in Scotland was weighted against Catholics.
"The proposal that shared campuses are the solution clearly suggests that standalone campuses are a problem. This is demonstrably not true," he said.
Nil By Mouth campaign director Dave Scott said: "Educational initiatives must be at the very heart of any successful anti-sectarianism strategy and shared campuses have proved very successful where they have been tried.
"They promote greater community cohesion and help break down barriers between young people from different religious and cultural backgrounds.
"Given the current difficult economic climate there is also a strong economic case to be made for their greater use."
Nil by Mouth's 13-point plan also includes a compulsory rehabilitation programme for anyone convicted of sectarian offences and calls for funds for supporters' groups to develop their own projects.
The charity wants every civil servant and school pupil in Scotland to receive dedicated sectarianism awareness training by 2015. It also calls for research into the link between Old Firm matches, domestic abuse and injuries to children.
Nil by Mouth was set up by Glasgow teenager Cara Henderson following the murder of her friend Mark Scott.
Glasgow and seven other councils – Argyll and Bute, Dumfries and Galloway, East Lothian, Highland, Inverclyde, North Ayrshire and North Lanarkshire – are in talks with the Scottish Futures Trust to build shared campus schools.
Under the projects, schools remain separate, but pupils share facilities such as libraries, dining and sports halls and pitches to save money.
The idea of shared campuses first sparked controversy in 2003 when senior education staff in North Lanarkshire unveiled a £150 million plan that included the creation of seven joint-campus primary schools.
The Catholic Church objected because some designs did not allow for separate public entrances, staff rooms and offices it felt were necessary for Catholic schools to retain their separate ethos and identity.
However, the Scottish Government said it had found no legal justification for the church's claim the proposals could lead to a "significant deterioration" in the educational provision of Catholic schools.
A report by independent consultants, commissioned by the council and published in 2007, found the majority of parents and school staff thought the policy had been successful, although there were concerns over facilities that did not relate to the shared-campus aspect of the schools.
"In the Roman Catholic schools, the shared campus did not create difficulty in implementing the Catholic Education Commission's charter for Catholic schools," the report stated.