Detainees leaving the facility waited at bus stops for rides and wondered where they would live after being banned from Tel Aviv and Eilat, where African migrant communities have sprung up.
The mayor of a third city warned that freed migrants would be prevented from entering his town.
One man said he was leaving the Holot Detention Centre with just USD 17 and a sandwich.
The supreme court ordered Israel to release illegal migrants held for more than a year at the detention centre in the Negev desert, in a ruling that affected 1,178 asylum seekers.
Authorities have barred those freed from entering Tel Aviv and Eilat in the face of hostility from many residents.
As in other parts of the world, illegal migration has become a high-profile issue in Israel, with rightwing politicians calling for action to limit it and activists urging the government to accept people from countries such as Eritrea.
"We don't know where to go, where we're going to sleep tonight," said Salah, a 33-year-old Sudanese man who has been in Israel for nine years, including 20 months at the detention centre.
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