The judge hearing that case pushed the rules back to the CFTC, after he determined the regulator failed to determine if the rules were necessary before writing them. The CFTC is mulling an appeal.
The Republican lawmakers saw that court case as an indication the agency was diverting valuable resources to efforts they believe are unnecessary, taking away from its core mission.
The regulator's "inability to adhere to the law" was evident in the loss in court, they argued.
"We are very concerned, in the wake of the financial crisis, that CFTC staff are using limited resources to pursue ideological and political goals rather than using the resources allocated by Congress to carry out the direct requirements of the agency," they wrote.
Gensler has maintained the regulator is trying to implement Dodd-Frank by establishing position limits in a bid to curb speculation. After the court ruling, he called the rules "critically important."
The letter also continues an ongoing battle between House Republicans and the CFTC over the agency's budget. The president's fiscal 2013 budget request included a substantial boost to the CFTC's funds, to allow it to handle its increased workload after Dodd-Frank. But Republicans controlling the House have actually sought to trim the CFTC's budget from existing levels.
The lawmakers behind the letter accused the CFTC of "serious mismanagement" of its existing funds in pursuing such rules and defending them in court. They asked for details on how much staff time was spent drafting and defending the position limit rules.