Egyptian President Mohammed Morsi ordered military forces to the region after 16 soldiers were killed in an attack along the Israeli border last month. The Sinai Peninsula has existed in a lawless state since the Egyptian revolution in 2011.
Human Rights Watch said sub-Saharan migrants were subjected to torture and sexual assault in an effort to secure ransom from their relatives.
Joe Stork, deputy director of Middle East and North African affairs at Human Rights Watch, said thousands of asylum-seekers feel into the hands of human traffickers in the Sinai.
"Egypt's new government should use its increased law enforcement operations to rescue victims of trafficking and end these abuses," he said in a statement from New York.
Egyptian news agency al-Ahram reports that authorities were reaching out to Islamic rebels in the Sinai in an effort to find a resolution to the lingering crisis in the region.
Egyptian forces pulled back from the region during a holiday season marking the end to the Islamic holy month of Ramadan. Dubbed Operation Eagle, military sources told al-Ahram a new tactical deployment was under way that would take advantage of "fresh intelligence."