The two, Ranjan Mohanta and Ghanashyam Mohanta, were acquitted for lack of evidence in the burning to death of the missionary and his two sons on January 22, 1999 when they were sleeping in a station wagon at Manoharpur village in the district.
Judge B C Rath set the accused free after CBI could not substantiate evidence against them, defence lawyer Bana Bihari Mohanty told reporters.
They were arrested from their villages in Keonjhar district on May 13, 2013 by the CBI who had been chasing them for 14 years. Another accused Budhia Naik is still at large.
CBI had filed charge sheets against 18 persons including prime accused Dara Singh alias Rabindra Kumar Pal.
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Earlier, the district and sessions court in Khurda had awarded death penalty to Dara and lifer to 12 others.
Later, the Orissa High Court reduced the death sentence of Dara to life imprisonment and upheld the lifer for Mahendram on May 19, 2005.