The second suspect, named as Justin Kambare, was "currently being interrogated", Kazarama said.
The two suspects belonged to the tribal Mai-Mai Pareco militia, the army spokesperson said.
"The motive being put forward is that Monusco was blocking their integration into the FARDC forces [Armed Forces of the DR Congo]."
A disarmament and integration deal for militia groups in the east of the country is part of a wider peace deal with the government.
Ban Ki-moon, the UN secretary-general, had condemned the attack and called for Congo's government to launch an immediate investigation.
He also sent condolences to the Indian government and the families of the three soldiers, and expressed his support for the UN peacekeeping mission. The UN security council issued a similar statement.
Nearly 4,000 Indian army soldiers are part of the UN Congo peacekeeping mission, which has about 20,000 people from various countries.
The mission has lost more than 100 peacekeepers since 1999.
DR Congo's president has said that he wants all the peacekeepers out before September 2011 and the UN approved a partial withdrawal earlier this year.
John Holmes, the UN humanitarian chief, has warned that violence in the east of the country may spiral out of control if the peacekeepers all leave.
Rebels ousted longtime dictator Mobutu Sese Seko in 1997, then turned on each other in back-to-back civil wars that became an international scramble for the country's minerals and drew in soldiers from more than a half-dozen African nations.
The $1.35 billion-a-year UN mission helped hold DR Congo's first democratic elections in 40 years in 2006, although results were disputed and critics said the process favored the incumbent, Joseph Kabila.