In the 1994 parliamentary election, he contested the Kathmandu-3 constituency. Singh won 33.77% of the votes in the constituency, but was defeated by the CPN(UML) candidate Manmohan Adhikari.[6]
Singh was removed from his ministerial position when King Gyanendra took power in February 2005. In February 2005, Singh was arrested for two weeks. Singh was again arrested on April 21, 2005, after refusing to appear for a hearing of the Royal Commission for Corruption Control. Singh, along with Sher Bahadur Deuba, were accused by the RCCC of involvement in a case of corruption relating to the Melamchi Drinking Water Project. Singh had refused to appear in front of the RCCC, as he considering the institution as unconstitutional.[10][11] In July 2005, Singh and Deuba were sentenced to 2 year in jail and a fine of 90 million rupees. Singh was released from jail on February 13, 2006, as the Supreme Court of Nepal ordered the dissolution of the RCCC.[12][13]
In the 12th General convention of the Party held on September 22, 2010, Singh was elected as General Secretary of the Party defeating rival candidate Bimalendra Nidhi from Deuba Camp.[18]
Singh, the son of Ganesh Man Singh fielded candidacy for the post of party president leaving the camp in the 14th general convention of Nepali Congress.[19] He was able to garner nearly 7% voters opening the way for second round of election as Deuba who obtained 48% votes was unable to cross 50% mark even joining hands with leader Krishna Prasad Sitaula.[20] Later, Deuba asked Nidhi and Singh for support while Singh said he was ready to support Deuba.[21] With this, Deuba and Singh came together after almost 12 years.[22]