Mortgage firms Fannie Mae and Freddie Mac face a unique set of problems that distinguish them from other firms receiving government aid when it comes to setting executive pay, the Obama administration's pay czar said on Wednesday.

Kenneth Feinberg, the Treasury Department official charged with overseeing executive pay at firms receiving aid from the government's $700 billion bailout fund, told CNBC the uncertainty over the future of the mortgage finance companies was one factor that made their situation unique.

One, there is no stock, so all of the compensation needs to be in cash ... And secondly, the future of Fannie and Freddie politically remains very uncertain and as a result of that, it's very difficult to convince people to come to work for Fannie and Freddie when they don't know how long there will even be a Fannie and Freddie, he said.