New governing documents will include a provision for the payment of pastors who are also trustees and will ensure their salaries are "transparent and accounted for".
The commission said that problems at "high-profile independent churches in London" had revealed that many governing documents of evangelical organisations were "insufficient for good governance".
This month, the commission censured another evangelical Christian charity for overpaying its pastor. Power Praise & Deliverance Ministries International gave its pastor a £60,000 pay rise in 2001, despite the fact that he spent half of the previous year abroad and it was losing members.
The charity had been registered on the understanding that its pastor's salary would be "on a similar level to a Church of England vicar". But it hiked his salary from £15,464 in 2000 to £75,359 in 2001. He also received free accommodation.
The report into the north London church comes soon after another report ordered Pastor Matthew Ashimolowo to repay £200,000 to the Kingsway International Christian Centre following a damning inquiry into "unauthorised trustee benefits".
The draft governing documents for non-denominational churches were developed in consultation with the Evangelical Alliance, the African Caribbean Evangelical Alliance, Stewardship Services and the Penial Church.
A 'remuneration clause' allows for one or more pastors to be paid, but requires explicit authority for all trustee benefits and that "any potential conflict of interest is properly and openly managed".
R David Muir, director of public policy at the Evangelical Alliance, backed the new rules. "Trustees have to separate their own personal interests from the interests of the charity," he said.
"Congregational generosity should not be abused."