The information was released in response to a freedom of information request by the Belfast Telegraph.
OFGEM said the investigations focused on what appeared to be "ineligible installations".
All three investigations are ongoing.
The other two cases involved suspected frauds with values of £350,000 and £48,000 respectively.
When they are finished a decision will be taken on whether to refer them to police.
The Police Service of Northern Ireland has already said that it is in contact with OFGEM and the Department for the Economy over the referral of suspected fraud cases at the earliest opportunity.
It has said so far neither has indicated they had identified a case which showed criminal conduct.
The RHI scheme was intended to increase the creation of heat from renewable sources.
However, businesses have been receiving more in subsidies than they are paying for renewable fuel and the scheme became majorly oversubscribed.
The fallout from the scandal surrounding the scheme, which is approximately £490m over budget, resulted in the resignation of Sinn Fein's deputy first minister, Martin McGuinness, the collapse of Stormont's institutions and the calling of snap elections on 2 March.
Retired appeal court judge Sir Patrick Coghlin will chair a public inquiry into the botched energy scheme.
The body which regulates the controversial Renewable Heat Incentive (RHI) scheme has confirmed it is investigating three cases of suspected fraud including one with a potential value of £2.5m.