JACKSON (AP) — The federal housing program that began in the aftermath of 2005’s deadly hurricane season ends Friday, but many residents along the Gulf Coast will likely remain in government-issued trailers, at least for a while.

Nearly 5,000 families in Louisiana and Mississippi were still living in Federal Emergency Management Agency trailers on Thursday, despite the agency’s order to vacate by a May 1 deadline.

FEMA will hand deliver notices Friday, ‘‘informing those who remain that they must surrender the housing unit or FEMA will ask the U.S. Department of Justice to pursue legal action to gain possession of the housing unit,’’ FEMA spokesman Eugene Brezany said in an e-mail.

FEMA also will stop paying the costs of 137 families living in motels and hotels in those states. There were 19 families living in hotels in Alabama as of Thursday.

‘‘As applicants move out of FEMA units and into their long-term housing resource, FEMA is deactivating and removing the mobile homes, park models and travel trailers,’’ Brezany said.

FEMA said the $5.6 billion housing assistance program was the largest federal temporary housing operation in the nation’s history. At its peak, 143,000 households along the Gulf Coast were living in temporary housing units.

Affordability has been the main hurdle to finding permanent housing for many displaced by Hurricane Katrina. Rent more than doubled along the Mississippi Gulf Coast. Much of the affordable housing stock was destroyed and insurance rates increased.

Stephen Carr, director of the Mississippi Case Management Program, which was created to assist in the state’s post-Katrina housing recovery, said his organization has been trying to help hotel tenants find other options, including staying with family and friends. Some are being placed in rental units, using housing subsidies from nonprofits.

‘‘We’ve not been told of any strategy that they’re going to begin pulling travel and mobile homes on May 1. They’ll coordinate with the family to let them know when the units are going to be picked up. I don’t anticipate that happening in the first month,’’ Carr said.

As of Thursday, 1,849 Mississippi households were living in FEMA trailers. In Louisiana, there were 3,006.

‘‘It is our understanding that for families in trailers on May 1, FEMA is going to be working with them on a one-on-one basis,’’ said Christina Stephens, a spokeswoman for the Louisiana Recovery Authority.

Stephens said her staff has been calling families in hotels, ‘‘looking for any ’stop gap’ measures for those who might not have a place to stay.’’ She said the state might have housing funds available until the families find permanent shelter.

Brezany said he didn’t want to give residents the impression that the agency was extending the program. He said tenants are encouraged to work with the state case management service, which is available until June 1.