In Pacifica vs FCC, the Justice Department took the position of Pacifica over the FCC. ⚖

It turns out that the Justice Department doesn’t have a legal obligation to defend or support the position of an Independent federal agency. This is because the president has no direct say over an independent agency, so his justice department has the right to either support or oppose the actions of the agency.

While sometimes the Justice Department chooses to not defend a federal agency in court, they can’t normally take the side of a defendent or claimant against a federal agency.