The top federal agencies responsible for setting housing policy are clashing over a new program designed to help borrowers whose homes are worth less than they owe on their mortgages, according to industry and government sources. The Federal Housing Administration says the program could avert foreclosures, but the Federal Housing Finance Agency has concerns that the program, if expanded to include the government-controlled mortgage giants Fannie Mae and Freddie Mac, could be a logistical nightmare that would cost taxpayers too much, the sources said. About one in four borrowers is underwater. Without equity in their homes, these borrowers tend to be vulnerable to foreclosure because it is difficult for them to refinance or sell their homes. Housing advocates have said that helping these borrowers is important to stem the nation’s foreclosure tide.