A regulatory case report by the commission said the charity's decision to carry out research last year for former Liberal Democrat leader Sir Menzies Campbell MP, which was used for a party publication, was "not appropriate" and did not further the charity's public benefit objectives.
The Royal United Services Institute is a well-known defence and security think tank formed in 1831. It appointed former head of the British Army, Sir Richard Dannatt, as its chair earlier this month.
After the matter was referred to it by the Electoral Commission, the Charity Commission opened an investigation in March.
The investigation concluded that the research constituted support for Campbell and the Liberal Democrats because it was used as the basis of a party political publication and was not made available to other politicians, parties or members of the public.
But it accepts that the charity did not intend to support the MP or the party.
The case report says it was "difficult to see how the trustees had discharged their legal duties and responsibilities to charity in making the decision to undertake the research commissioned exclusively by and for the MP".
The institute has since amended its internal procedures for interaction with politicians to ensure a similar situation does not occur again.
In a statement, the institute said it had sought to protect itself from creating the perception that it was providing support to a political party through a contractual obligation that it remained anonymous. However, it says this agreement was overlooked when the paper was published.