About 15,000 refugees and migrants from Asia and North Africa have passed through Bosnia this year on their way to Europe's wealthier countries.
"The key challenge now is how to prepare for winter," said Stephanie Woldenberg, senior protection officer for the UNHCR refugee agency.
"It is the race against time and UNHCR is particularly concerned about vulnerable families and individuals who are most at risk."
Woldenberg, speaking at an event sponsored by the Organization for Security and Cooperation in Europe (OSCE), said more than 1,000 refugees and migrants were sleeping rough in Bihac and Velika Kladusa, two towns in the northwestern Bosnia near the Croatian border, Reuters reported.
Several thousand migrants remain in Bosnia after Croatia tightened its borders and new people arrive daily, crossing illegally from Serbia.
Bosnia's state authorities say they are coping to refurbish inadequate facilities where migrants are currently accommodated but the process has been slow because of a lack of funding and cooperation from local counterparts.
Woldenberg said a priority for the authorities was to protect families with children, single women and unaccompanied minors. "Safe appropriate accommodation must be provided for these groups as a priority," she said.