The board of 24-7 Prayer International has suspended CEO Mike Andrea following "serious allegations of historic misconduct".
The allegations have come from former members of Global Generation Church in Thanet, Kent, which has also suspended Mr Andrea from his leadership role.
The board met on November 16, the day after a former member of the church posted allegations online.
"We unanimously agreed to suspend Mike Andrea immediately in order to conduct an investigation with the benefit of professional, independent counsel," the 24-7 trustees said in a statement.
They said the allegations "relate to events prior to 2011, before Mike's appointment as CEO of 24-7 Prayer in 2019".
The board indicated that before their decision to suspend Mr Andrea, they had been made aware of other allegations "from several other former church members over recent weeks, which have become the subject of an ongoing investigation by the elders and trustees of Global Generation Church".
"We take all such allegations as matters of the gravest concern," the trustees said.
They added: "At the present time there have been no allegations of impropriety relating to Mike Andrea's role as operational head of 24-7 Prayer International."
Global Generation Church's board of elders and trustees also issued a statement saying, "Yesterday allegations were posted online, against Mike and Stella Andrea, leaders of Global International Church in Thanet. The allegations have been made by a former member of the church and relate to events prior to 2011."
The board said it had suspended Mr and Mrs Andrea "immediately", and that it was committed to "an independent and thorough process".
The statement confirmed: "We have been made aware over the last few weeks of allegations against Mike Andrea from several former church members.
"These have been the subject of an ongoing investigation by the elders and trustees of Global Generation Church.
"This process has been in consultation with our external advisor from 24-7 Prayer International.
"This will be reviewed by an independent professional organisation specialising in this level of complaint. We will commit to an independent and thorough process."
Mike Andrea has been contacted for comment.