HOUSTON — The federal government has adopted guidelines intended to prevent prison rape in part by separating young offenders from adult inmates. But four years after the rules were supposed to take effect, they are proving difficult to adopt in the nation’s crowded jails and penitentiaries.

Since 2012, states have been working to meet the standards set forth by the Prison Rape Elimination Act, or PREA, which was partly inspired by the 1996 death of Rodney ­Hulin, an undersized 17-year-old inmate who hanged himself in Texas after his requests for help after repeated rapes by adult inmates were denied.

Texas sheriff’s offices say separating the two populations has been a challenge because of overcrowding and steep financial costs.

‘‘It’s a big logistical headache,’’ Brazos County Sheriff Chris Kirk said.

The law was also supposed to provide for better staff training, improved reporting and investigation of all sexual assaults behind bars, and more money for research.

In 2011-2012, an estimated 4 percent of state and federal inmates and 3.2 percent of jail inmates reported experiencing one or more incidents of sexual victimization by another inmate or facility staff, according to the Justice Department.

The rape-prevention law ‘‘is a valuable and important act, and we take it very seriously,’’ said Ryan Sullivan, a spokesman for the Harris County sheriff’s office, which has about 150 youth offenders at its jail in Houston. The facility holds more than 9,000 inmates.

The Harris County Jail was cited in a May audit for not housing 17-year-old offenders apart from adult inmates. Elsewhere in Texas, Dallas County is spending more than $11,000 per week to keep at least 60 juveniles separated from adults at its jail complex.

The nation’s 7,600-plus prisons, jails, community-based facilities, and juvenile detention centers are being checked on their compliance with the law. So far, only 12 states are in full compliance, according to the Justice Department. Thirty-six other states say they are working to comply.

Still, the department said it is sees ‘‘evidence of a very substantial effort nationwide’’ to satisfy the new standards.

The age separation has been especially complicated in states such as Texas that prosecute 17-year-olds as adults. Advocates say some facilities still question whether the federal mandate applies to them.

In many jurisdictions, one of the biggest barriers is summoning the political will to make changes, said Brenda Smith, who was a member of the National Prison Rape Elimination Commission, which helped develop the standards.

States that do not comply face losing 5 percent of their federal prison grants. County jails and local lockups are usually not included in the determination of whether a state is in compliance. Locally run facilities have no risk of losing federal money unless that funding is directly tied to a state contract for jail services.