Some 300 members of the troubled north African country's armed forces have been based at the Bassingbourn Barracks in Cambridgeshire, since July.
"Training was initially expected to last until the end of November but we have agreed with the Libyan government that it is best for all involved to bring forward the training completion date," the ministry said in a statement.
"The recruits will be returning to Libya in the coming days."
Three of the Libyan soldiers -- Ibrahim El Maarfi, Mohammed Abdalsalam and Khaled El Azibi -- were due in court in Cambridge on Tuesday.
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Maarfi and Abdalsalam have each admitted two counts of sexual assault. Azibi has been charged with three counts of sexual assault but has yet to enter a plea, British media reported.
Two other servicemen, Moktar Ali Saad Mahmoud and Ibrahim Abogutila, have been charged with raping a man, the Cambridge News website reported.
"The majority of recruits have responded positively to the training despite the ongoing political uncertainty in Libya but there have been disciplinary issues," the ministry said.
It said the government would now "review" whether to continue training Libyan recruits in Britain.
Local MP Andrew Lansley said he had written to the MoD to raise his concerns and warned he would oppose any more Libyan troops being hosted at the base.
"It is clear that the stipulation that there was to be no unauthorised exit from the base has not been adhered to and the consequences have been unacceptable," he said.