The issue was raised by Swaraj during a meeting with her Myanmarese counterpart U Wunna Maung in which both the leaders reviewed the bilateral ties.
"I raised the issue of Indian insurgent groups and told them that though the political leadership is again and again saying that their territory will not be used for terrorist activities, but on the ground, the situation is different," she told reporters.
The External Affairs Minister also raised the issue with Myanmar's President U Thein Sein when she called on him.
"The President categorically said that Myanmar will never allow its territory to be used for anything that is inimical to India's interests," Spokesperson in the Ministry of External Affairs Syed Akbaruddin said.
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He said both sides would focus on operationalising an MOU which provides for intelligence sharing and cooperation between security forces of the two neighbours.
India shares around 1,600 kms of border with Myanmar and most of it is unfenced.
North East militant outfits United Liberation Front of Asom (ULFA) and a number of other insurgent groups are reported to have training camps in northern Myanmar.
The two sides deliberated on various issues including ways to increase bilateral trade and investment and improve road, sea and aerial connectivity.
Swaraj sought early implementation of trilateral highway project between India, Myanmar and Thailand and suggested flight services from Delhi to Yangon via Bodh Gaya.