Italy holds people at the camps who have been picked up or rescued trying to cross the Mediterranean from North Africa.
In January, hundreds of asylum-seekers and hopeful migrants broke out of one of the holding centres and marched peacefully to the island's town hall to demonstrate about their conditions.
They were joined by a few hundred locals who also want the inmates transferred to bigger camps elsewhere in Italy.
At the time, the United Nations high commissioner for refugees (UNHCR) expressed concern over conditions at the centre.
The UNHCR said it had been built for 850 people but now had up to 2,000 crammed in, many sleeping under plastic sheets.
Barrot will visit Lampedusa on Friday to assess conditions. He will also hold talks with Roberto Maroni, the Italian interior minister, in Rome.