Army officials and militants had previously denied such contact despite pledges on both sides to end the conflict in the region after the Federal Government combined a military offensive with amnesty offer to tackle growing violence.
The unrest has shut down between 500,000 and one million barrels a day of crude production in the country.
Colonel Usman Yusuf, an area commander for the JTF, said: "We are in contact with three groups." The JTF spokesman couldn't be reached for comment, according to allafrica.
Yusuf said his area of responsibility covered KalabariKingdom, in RiversState - the state with the largest oil production in the Niger Delta. He said the groups he is talking to are located in Elem Minama and Kula. Both communities are close to pipelines operated by a Royal Dutch Shell Plc unit that were attacked last year.
The colonel said he was discussing the "conditions to drop their weapons and how to collect" them. For now, he said he has an understanding with the militants he is talking with that "we won't shoot at them, and they won't shoot at us."
Yar'Adua is due to release a report detailing the conditions for the amnesty this week.
But Yusuf said the "release of the final report is not a condition to accept the amnesty. They can accept the amnesty now and come back to live freely as citizens."
Yar'Adua moved in April to modify Federal Government's approach to armed struggle in the Niger Delta, by proposing amnesty for militants who turn their backs on militancy.
The President's proposal will be discussed at the National Council of State (NCS) and other relevant levels of political authority.