Investigation by the regulator comes to light in Kingsway International Christian Centre's most recent accounts
The order has been made by the commission as part of a statutory inquiry it started into the charity last year after concerns were raised about its financial controls.
It is the second inquiry into the charity by the commission, which concluded in 2005 that there had been a "possible misapplication of funds" by the senior pastor Matthew Ashimolowo, who agreed to repay £200,000 to the charity.
The church is based in east London and claims an attendance of up to 12,000 people a week at its main building in Walthamstow. It has several other branches and its income in 2010/11 was £9.4m. In 2010 it lost a planning bid to convert a former bingo hall in Crystal Palace into a new church,
The new inquiry, which is continuing, is mentioned in the charity's latest accounts filed with the commission, which reveal that it gave £5m to a former trustee, the former professional footballer Richard Rufus, to invest in the financial markets.
The accounts say the investments, made in two instalments of £3m in 2009/10 and £2m the following year, reaped returns of £836,720 in the first year and £500,000 in the second.
They also say that, in the wake of the commission’s investigation, trustees sought professional advice and took "the prudent step of providing for losses on the capital amount invested".
Nick Brooks, head of not-for-profit at accountancy firm Kingston Smith, said it was not clear from the latest set of accounts if the £5m investment had been lost, but there appeared to be some doubt about whether the charity would get it back.
He said there were wider questions posed by the situation such as what type of evaluations had been taken before trustees agreed to the investments.
A spokeswoman for the Charity Commission said: "The Charity Commission opened a statutory section 8 inquiry into the charity the Kingsway International Christian Centre on 11 February 2011 following concerns raised about the charity’s governance and internal financial controls, in particular relating to investments.
"The commission is in contact with the trustees concerning this matter. As a precaution, the charity has to obtain prior written permission from the commission before making investments, which does not prevent the charity from conducting normal day-to-day activity."KICC was previously investigated by the commission under its old name of King's Ministries Trust. The investigation lasted three years and cost £1.2m.
The 2005 commission report, which said there had been a "possible misapplication of funds", found that the charity spent £120,000 celebrating Ashimolowo's birthday and that he used the charity’s Visa card to buy a timeshare apartment in Florida.The charity declined to comment.