Elizabeth Mockus and Sandra MacKenzie, who share the headship at Kirktonholme Primary in East Kilbride, have been moved to other duties to allow South Lanarkshire Council to investigate.
The issue came to light after Alex Gear, from the West Mains Church of Christ, a US-based sect that does not believe in evolution and condemns gay relationships, was invited to become one of the school's chaplains.
Mr Gear also ran a club at the 400-pupil school on Monday evenings and spoke to pupils about his beliefs as part of their religious education lessons.
Many parents only realised their children were being exposed to the evangelical group's agenda when pupils took home creationist books they had been handed at assembly.
Following the revelations, parents called for the headteachers to be sacked at an angry public meeting.
Yesterday, Jim Gilhooly, the council's director of education, said: "As indicated to parents, a full investigation into the management practices within the school has been instigated.
"In order to assist with this, the current headteachers have been moved from the school and re- deployed to other duties within education resources with immediate effect. A temporary senior management team has been put in place.
"The council will continue to work with the parents to ensure that Kirktonholme Primary School now moves forward with educating and caring for the community's children."
In a separate letter to parents, Mr Gilhooly has also committed to investigating the membership, role and functioning of the church group leaders in the chaplaincy team at the school.
The inquiry will further look at the use of the school premises for the youth club run by the West Mains Church of Christ.
The letter states: "It has been agreed that the West Mains Church of Christ will no longer access lets in schools for the youth club, or any other activity.
"In my discussions with the parent council, and during the larger parent meeting, it was clear that everyone was keen to see the school move on from the current situation.
"Hopefully these initial actions help to achieve this and I want to assure you that the safety and education of your children are paramount in all of our minds."
The scandal blew up after two creationist books denouncing the theory of evolution - one called How Do You Know God is Real? and the other entitled Exposing the Myth of Evolution - were handed out to pupils.
Both were written by American author Kyle Butt, whose other works include a book called Homosexuality - Sin or Cultural Bad Habit? His books are printed by the Alabama-based Apologetics Press, which is closely affiliated to the Church of Christ.
In a subsequent letter to parents, which was given out after the books were given to pupils, Mrs MacKenzie defended the decision to give the books to pupils.
She said: "While I appreciate that not every family in our school are practising Christians, I was only too happy to accept this generous gift on your behalf. I hope you will all accept it in the spirit with which it was offered."
However, some parents made official complaints to the council about the books, while others threatened to withdraw their children in protest.
The Church of Christ, based in Alabama, believes the Bible predicts the future and is 100% accurate. It has called Scotland "a field ripe for harvest".