The RSPCA came under fire last month after it spent more than £320,000 on a successful private prosecution of the Heythrop Hunt in Oxfordshire for illegal fox hunting.
District Judge Tim Pattinson, presiding over the case, said that members of the public might feel that the charity's funds could be "more usefully employed".
In a letter to the commission sent last month, a cross-party group of politicians accused RSPCA trustees of failing in their "duty of prudence" to the organisation and its funds, and called on William Shawcross, chair of the commission, to investigate.
In a reply to the politicians, seen by Third Sector, Shawcross said: "Given the concerns raised by the judge, by yourselves and by others, we are seeking an early meeting with the RSPCA to discuss their approach to prosecutions in general and to this case in particular."
A commission spokeswoman confirmed that members of staff were to meet the RSPCA this week to discuss its approach to prosecutions, but said that decisions on prosecutions were for trustees of charities to make, and they would not normally be a regulatory matter for the commission.
She added: "We are not investigating the charity, nor do we have regulatory concerns about the charity at this point."
The RSPCA did not respond to requests for comment about the meeting before Third Sector's deadline.
Last month, Gavin Grant, the chief executive of the RSPCA, revealed the charity had launched a separate fighting fund to help avoid future criticism about using regular supporters’ money to pay for private prosecutions.