Organisations that monitor the situation in Libya fear these closures may lead to even more overcrowding in the remaining centres.
They also fear the possibility of many more migrants being left in the hands of traffickers.
The UN last month called for the dismantling of all detention centres for refugees in Libya, saying the facilities were not fit to house migrants.
Campaign group Amnesty International has called conditions “horrific” and “inhuman”.
Detainees in various centres have described routine torture, rape, malnutrition and the spread of diseases like tuberculosis due to the conditions they are forced to endure.
Libya’s plans to close the three centres follows criticism that migrants were being returned to Tajoura after it was hit by a deadly missile attack in July.
That “outrageous” attack could amount to a war crime, said the UN’s Libya envoy Ghassan Salamé and top human rights official Michelle Bachelet.
But the UN Security Council failed to condemn it after the US declined to endorse a joint statement, according to diplomats.
Tajoura Detention Centre is close to the capital, Tripoli, where there is ongoing fighting between the UN-recognised government and the Benghazi-based Libyan National Army which has vowed to take over the city.
Only last week, 150 migrants drowned after they left Libya for Italy.
This was the largest loss of life in the Mediterranean Sea this year.
On Thursday, 52 migrants including 16 women and two babies were rescued from a ship that was in danger of sinking halfway between Libya and Italy.
Spanish authorities have previously warned the charity which conducted the rescue, called Proactiva Open Arms, to stop its search and rescue missions of face fines of up to 900,000 euro ($999,000; £825,000).