A case was also registered against the former director of the MDS and an official for their alleged financial misappropriation.
Mr Singh and the other accused have been charged with cheating, criminal conspiracy and breach of trust. The charges for breach of trust is non-bailable and are liable to be punished with three years of imprisonment.
The case against them alleges financial irregularities amounting to Rs 185.79 crore.
A Vigilance Commission report, on recommendation of the chief minister's office, named six people, stating that they are required for examination in the investigation into the alleged financial irregularities.
Apart from Mr Singh, three former chief secretaries - DS Ponia, PC Lawmkunga and O Nabakishore Singh, a former project director of MDS, Y Ningthem Singh, and administrative officer of MDS, S Ranjit Singh have been named in the FIR. While Mr Poonia and Mr Lawmkunga are retired members, Nabakishore Singh is currently the director of State Academy of Training.
Mr Singh might move the Manipur High Court for anticipatory bail, sources said.