Basil Rajapaksa's remarks came while addressing reporters in Jaffna to launch Sri Lanka People's Party (SLPP), the new party of the Rajapaksa loyalists who want to breakaway from President Maithripala Sirisena's Sri Lanka Freedom Party.
He also accused the current Sirisena government of duping the Tamil community after getting their help to win elections in 2015.
"Our troops did not do war crimes. There may have been individuals who did the crime," Basil said in Jaffna, the first visit since January 2015 when Mahinda Rajapaksa was voted out of power in the presidential election.
He said the issue of disappearances of individuals needed to be resolved and accused the main Tamil party Tamil National Alliance (TNA) of not having cooperated with the Rajapaksa government to help the Tamils.
"Now they have leader of the opposition's position and all they do with it is to support the government in everything this government does without addressing the Tamils' problems", Basil said.
Sri Lankan troops have been largely accused of committing war crimes during the final battle in May 2009.
Three successive UN Human Rights Council resolutions have urged for independent international investigations into war crimes blamed both on the government troops and the LTTE.
According to the government figures, around 20,000 people are missing due to various conflicts including the 30-year- long separatist war with Lankan Tamils in the north and east which claimed at least 100,000 lives.
The LTTE, which led the separatist war for a separate Tamil homeland, was finally crushed by the Lankan military in 2009 with the death its supremo Velupillai Prabhakaran.
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