He triggered controversy amid the protests over the police action at Jawaharlal Nehru University (JNU), on 14 February 2016, claiming that the "JNU incident" was supported by Lashkar-e-Taiba chief Hafiz Saeed. He gave the statement when there was an Anti-National speeches in the JNU Delhi over the anniversary of hanging of Kashmiri Separist Maqbool Bhat and Afzal Guru on 9 February 2016. After the statement there was also a vast protest against Singh and after the arrests of Umar Khalid and Kanhaiya Kumar, he made meeting with many left leaders. He also assured the citizens that what he said was right and he also people assurance of not tolerating the Anti-National Acts. Singh at that time also appointed an SIT for the investigation of the matter.
In May 2016, he claimed that infiltration from Pakistan declined by 52% in a period of two years.
Dassault Rafale is a fighter plane of French origin whose deal was signed by then Minister of Defence (India), Manohar Parrikar in 2016 to increase the strength of the Indian Air Force. The Government of India had signed to buy 126 fighter jets costing $30 billion. The planes were received during his tenure as the Defence Minister of India. Though that was also a very controversial issue, Singh received and completed the deal after becoming Minister of Defence of India and the Indian Air Force received its first Dassault Rafale on 8 October 2019, when he personally went to France to receive it. The first fleet of 5 fighter jets landed at Ambala Air Force Station.