The commission received a complaint from Comic Relief in April about the Busoga Association UK, a spokeswoman for the regulator said.
Busoga Association UK, which is based in Dalston, north-east London, runs community projects that support women in Uganda, and provides education and advice to people in the UK, the charity’s website says.
A spokeswoman for the Charity Commission said it was approached by Comic Relief with concerns that "insufficient accounting records had been made available" to confirm how grants Comic Relief had made to the charity were applied.
"The commission has sought a meeting with the trustees of the charity to discuss what evidence exists concerning the use of the funds in question, together with the charity’s governance and financial management arrangements," the spokeswoman said.
"Before that meeting, the commission has not formed a view of what the outcome will be in terms of any regulatory advice or action."
The spokeswoman for the regulator could not confirm the value of the grants given by Comic Relief.
A spokeswoman for Comic Relief confirmed that the organisation was in contact with the commission regarding an operational compliance case, but she said she could not comment on a case before its outcome.
"In our experience of making more than £800m of grants since 1985, cases of wilful misappropriation of funds are rare," she added.
Third Sector was unable to contact anyone at the Busoga Association UK for comment.