The document, signed by the BLF in February but published today, outlines the relationship between the regulator and the grant-making body and will allow for joint operations to be carried out by the two bodies.
The document says it is intended to "facilitate effective investigation and disclosure of information to prevent, detect and remedy misconduct or mismanagement in the administration of charities or charitable funds".
It will also promote effective working, communication and cooperation between the commission and the Big Lottery Fund, it says.
The document deals mostly with the exchange of information between the two organisations, including information about other charities.
It says the law allows the two organisations to share information to the extent that a joint operation between the two to look into a charity would be possible.
"Joint approaches can take place with the permission of the charity and every effort should be made to encourage the charity to take this option," the memo says. "If permission is refused, information exchange can still occur."
The organisations can exchange information, but the receiving party may not pass it on to third parties unless legally required to do so or the party giving the information agrees, the agreement says.
And the commission may not decide to share information with the BLF if that would have a detrimental effect on ongoing BLF investigations.
In "exceptionally serious" cases, the commission’s head of investigations and the BLF’s head of internal audit may designate a case as a coordinated operation, in which the exchange of information and expertise would continuous, the document says.
The commission could also pass the BLF information to inform the latter’s own investigation of charities, the agreement says, but this information could not be published by the BLF.
Both organisations will designate a person as a specific point of contact between the two bodies, and representatives from both organisations will be required to meet once a year to discuss strategy and consult on trends or problem areas, the agreement says.