According to a statement released by the ministry: "The majority of recruits have responded positively to the training despite the ongoing political uncertainty in Libya but there have been disciplinary issues.
"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 recruits will be returning to Libya in the coming days."
According to media reports, Maarfi and Abdalsalam have admitted to two counts of sexual assault, whereas Azibi has been charged with three counts.
Additionally, two other Libyan soldiers, Moktar Ali Saad Mahmoud and Ibrahim Abogutila, have been charged with raping a man.
Over 300 members of Libya's armed forces have been training at the Bassingbourn Barracks in Cambridgeshire since July, reported AFP News.
As per the ministry, the government will be reviewing whether or not to continue training Libyan troops in Britain following the recent developments.
"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," said local MP Andrew Lansley.
Lansley has written to the MoD warning that he would oppose any additional Libyan troops being hosted at the base.