The dialogue was led by National Security Adviser Ajit Doval and Indonesia's Coordinating Minister for Political, Legal and Security Affairs H Wiranto.
"India and Indonesia hold the first Security Dialogue, ... Both agreed on operational cooperation in security and counter-terrorism fields," External Affairs Ministry Spokesperson Raveesh Kumar tweeted.
Ahead of the dialogue, the Indonesian foreign ministry had said the two countries will discuss cyber security, counter-terrorism efforts and transnational organised crime.
Today's dialogue comes after Indonesia and India agreed to strengthen strategic partnerships across various key areas, including defence, security, economy and maritime at the 5th Indonesia-India joint commission meeting in Jakarta during External Affairs Minister Sushma Swaraj's visit last week.